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Sample records for surviving proteins compared

  1. Transcript and protein analysis reveals better survival skills of monocyte-derived dendritic cells compared to monocytes during oxidative stress.

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    Ilse Van Brussel

    Full Text Available BACKGROUND: Dendritic cells (DCs, professional antigen-presenting cells with the unique ability to initiate primary T-cell responses, are present in atherosclerotic lesions where they are exposed to oxidative stress that generates cytotoxic reactive oxygen species (ROS. A large body of evidence indicates that cell death is a major modulating factor of atherogenesis. We examined antioxidant defence systems of human monocyte-derived (moDCs and monocytes in response to oxidative stress. METHODS: Oxidative stress was induced by addition of tertiary-butylhydroperoxide (tert-BHP, 30 min. Cellular responses were evaluated using flow cytometry and confocal live cell imaging (both using 5-(and-6-chloromethyl-2,7-dichlorodihydrofluorescein diacetate, CM-H(2DCFDA. Viability was assessed by the neutral red assay. Total RNA was extracted for a PCR profiler array. Five genes were selected for confirmation by Taqman gene expression assays, and by immunoblotting or immunohistochemistry for protein levels. RESULTS: Tert-BHP increased CM-H(2DCFDA fluorescence and caused cell death. Interestingly, all processes occurred more slowly in moDCs than in monocytes. The mRNA profiler array showed more than 2-fold differential expression of 32 oxidative stress-related genes in unstimulated moDCs, including peroxiredoxin-2 (PRDX2, an enzyme reducing hydrogen peroxide and lipid peroxides. PRDX2 upregulation was confirmed by Taqman assays, immunoblotting and immunohistochemistry. Silencing PRDX2 in moDCs by means of siRNA significantly increased CM-DCF fluorescence and cell death upon tert-BHP-stimulation. CONCLUSIONS: Our results indicate that moDCs exhibit higher intracellular antioxidant capacities, making them better equipped to resist oxidative stress than monocytes. Upregulation of PRDX2 is involved in the neutralization of ROS in moDCs. Taken together, this points to better survival skills of DCs in oxidative stress environments, such as atherosclerotic plaques.

  2. Comparing survival curves using rank tests

    NARCIS (Netherlands)

    Albers, Willem/Wim

    1990-01-01

    Survival times of patients can be compared using rank tests in various experimental setups, including the two-sample case and the case of paired data. Attention is focussed on two frequently occurring complications in medical applications: censoring and tail alternatives. A review is given of the

  3. Comparative proteomic analysis of Salmonella enterica serovar Typhimurium ppGpp-deficient mutant to identify a novel virulence protein required for intracellular survival in macrophages

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    Kumagai Yoshinori

    2010-12-01

    Full Text Available Abstract Background The global ppGpp-mediated stringent response in pathogenic bacteria plays an important role in the pathogenesis of bacterial infections. In Salmonella enterica serovar Typhimurium (S. Typhimurium, several genes, including virulence genes, are regulated by ppGpp when bacteria are under the stringent response. To understand the control of virulence genes by ppGpp in S. Typhimurium, agarose 2-dimensional electrophoresis (2-DE combined with mass spectrometry was used and a comprehensive 2-DE reference map of amino acid-starved S. Typhimurium strain SH100, a derivative of ATCC 14028, was established. Results Of the 366 examined spots, 269 proteins were successfully identified. The comparative analysis of the wild-type and ppGpp0 mutant strains revealed 55 proteins, the expression patterns of which were affected by ppGpp. Using a mouse infection model, we further identified a novel virulence-associated factor, STM3169, from the ppGpp-regulated and Salmonella-specific proteins. In addition, Salmonella strains carrying mutations in the gene encoding STM3169 showed growth defects and impaired growth within macrophage-like RAW264.7 cells. Furthermore, we found that expression of stm3169 was controlled by ppGpp and SsrB, a response regulator of the two-component system located on Salmonella pathogenicity island 2. Conclusions A proteomic approach using a 2-DE reference map can prove a powerful tool for analyzing virulence factors and the regulatory network involved in Salmonella pathogenesis. Our results also provide evidence of a global response mediated by ppGpp in S. enterica.

  4. Acute traumatic coagulopathy decreased actual survival rate when compared with predicted survival rate in severe trauma.

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    Kim, Su Jin; Lee, Sung Woo; Han, Gap Su; Moon, Sung Woo; Choi, Sung Hyuck; Hong, Yun Sik

    2012-11-01

    To determine whether acute traumatic coagulopathy (ATC) should be combined with the trauma and injury severity score (TRISS) to predict outcome in severe trauma patients and investigate effects of the change in coagulation state during early resuscitation on the actual survival rate. This was a retrospective study. Significant variables that affected 28-day mortality were analysed using multivariate logistic regression. Study patients were classified into three groups: no coagulopathy, mild coagulopathy or severe coagulopathy. Concordance between actual and predicted survival rates were compared for each group. The predicted survival rate was calculated using the TRISS method. The study also determined whether changes in the coagulation state during inhospital resuscitation affected the relationship between actual and predicted survival in patients who had rechecked coagulation profile within 12 h after presentation. Data from a total of 336 patients were analysed. At presentation, 20.8% of the study patients had mild coagulopathy, whereas 7.7% had severe coagulopathy. Age, injury severity score, revised trauma score and presence of ATC at presentation were independently associated with 28-day mortality. Actual survival was significantly lower than predicted survival in the mild and severe coagulopathy groups. Aggravation of coagulation state from normal or mild to severe coagulopathy or persistent severe coagulopathy during inhospital resuscitation mainly contributed to the discrepancy between actual and predicted survival. ATC decreased actual survival more than expected. ATC should be combined with TRISS to predict trauma outcome in severely injured patients. Improvement in coagulopathy during resuscitation may reduce the incidence of preventable death after trauma.

  5. Individual survival curves comparing subjective and observed mortality risks.

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    Bissonnette, Luc; Hurd, Michael D; Michaud, Pierre-Carl

    2017-12-01

    We compare individual survival curves constructed from objective (actual mortality) and elicited subjective information (probability of survival to a given target age). We develop a methodology to estimate jointly subjective and objective individual survival curves accounting for rounding on subjective reports of perceived survival. We make use of the long follow-up period in the Health and Retirement Study and the high quality of mortality data to estimate individual survival curves that feature both observed and unobserved heterogeneity. This allows us to compare objective and subjective estimates of remaining life expectancy for various groups and compare welfare effects of objective and subjective mortality risk using the life cycle model of consumption. We find that subjective and objective hazards are not the same. The median welfare loss from misperceptions of mortality risk when annuities are not available is 7% of current wealth at age 65 whereas more than 25% of respondents have losses larger than 60% of wealth. When annuities are available and exogenously given, the welfare loss is substantially lower. Copyright © 2017 John Wiley & Sons, Ltd.

  6. Dinosaur Peptides Suggest Mechanisms of Protein Survival

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    San Antonio, James D.; Schweitzer, Mary H.; Jensen, Shane T.; Kalluri, Raghu; Buckley, Michael; Orgel, Joseph P.R.O. (Harvard-Med); (IIT); (NCSU); (UPENN); (Manchester); (Orthovita)

    2011-09-16

    Eleven collagen peptide sequences recovered from chemical extracts of dinosaur bones were mapped onto molecular models of the vertebrate collagen fibril derived from extant taxa. The dinosaur peptides localized to fibril regions protected by the close packing of collagen molecules, and contained few acidic amino acids. Four peptides mapped to collagen regions crucial for cell-collagen interactions and tissue development. Dinosaur peptides were not represented in more exposed parts of the collagen fibril or regions mediating intermolecular cross-linking. Thus functionally significant regions of collagen fibrils that are physically shielded within the fibril may be preferentially preserved in fossils. These results show empirically that structure-function relationships at the molecular level could contribute to selective preservation in fossilized vertebrate remains across geological time, suggest a 'preservation motif', and bolster current concepts linking collagen structure to biological function. This non-random distribution supports the hypothesis that the peptides are produced by the extinct organisms and suggests a chemical mechanism for survival.

  7. Comparative Analysis of Protein Domain Organization

    OpenAIRE

    Ye, Yuzhen; Godzik, Adam

    2004-01-01

    We have developed a set of graph theory-based tools, which we call Comparative Analysis of Protein Domain Organization (CADO), to survey and compare protein domain organizations of different organisms. In the language of CADO, the organization of protein domains in a given organism is shown as a domain graph in which protein domains are represented as vertices, and domain combinations, defined as instances of two domains found in one protein, are represented as edges. CADO provides a new way ...

  8. Intensive Hemodialysis Associates with Improved Survival Compared with Conventional Hemodialysis

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    Lindsay, Robert M.; Cuerden, Meaghan S.; Garg, Amit X.; Port, Friedrich; Austin, Peter C.; Moist, Louise M.; Pierratos, Andreas; Chan, Christopher T.; Zimmerman, Deborah; Lockridge, Robert S.; Couchoud, Cécile; Chazot, Charles; Ofsthun, Norma; Levin, Adeera; Copland, Michael; Courtney, Mark; Steele, Andrew; McFarlane, Philip A.; Geary, Denis F.; Pauly, Robert P.; Komenda, Paul; Suri, Rita S.

    2012-01-01

    Patients undergoing conventional maintenance hemodialysis typically receive three sessions per week, each lasting 2.5–5.5 hours. Recently, the use of more intensive hemodialysis (>5.5 hours, three to seven times per week) has increased, but the effects of these regimens on survival are uncertain. We conducted a retrospective cohort study to examine whether intensive hemodialysis associates with better survival than conventional hemodialysis. We identified 420 patients in the International Quotidian Dialysis Registry who received intensive home hemodialysis in France, the United States, and Canada between January 2000 and August 2010. We matched 338 of these patients to 1388 patients in the Dialysis Outcomes and Practice Patterns Study who received in-center conventional hemodialysis during the same time period by country, ESRD duration, and propensity score. The intensive hemodialysis group received a mean (SD) 4.8 (1.1) sessions per week with a mean treatment time of 7.4 (0.87) hours per session; the conventional group received three sessions per week with a mean treatment time of 3.9 (0.32) hours per session. During 3008 patient-years of follow-up, 45 (13%) of 338 patients receiving intensive hemodialysis died compared with 293 (21%) of 1388 patients receiving conventional hemodialysis (6.1 versus 10.5 deaths per 100 person-years; hazard ratio, 0.55 [95% confidence interval, 0.34–0.87]). The strength and direction of the observed association between intensive hemodialysis and improved survival were consistent across all prespecified subgroups and sensitivity analyses. In conclusion, there is a strong association between intensive home hemodialysis and improved survival, but whether this relationship is causal remains unknown. PMID:22362910

  9. Activated macrophage survival is coordinated by TAK1 binding proteins.

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    September R Mihaly

    Full Text Available Macrophages play diverse roles in tissue homeostasis and immunity, and canonically activated macrophages are critically associated with acute inflammatory responses. It is known that activated macrophages undergo cell death after transient activation in some settings, and the viability of macrophages impacts on inflammatory status. Here we report that TGFβ- activated kinase (TAK1 activators, TAK1-binding protein 1 (TAB1 and TAK1-binding protein 2 (TAB2, are critical molecules in the regulation of activated macrophage survival. While deletion of Tak1 induced cell death in bone marrow derived macrophages even without activation, Tab1 or Tab2 deletion alone did not profoundly affect survival of naïve macrophages. However, in lipopolysaccharide (LPS-activated macrophages, even single deletion of Tab1 or Tab2 resulted in macrophage death with both necrotic and apoptotic features. We show that TAB1 and TAB2 were redundantly involved in LPS-induced TAK1 activation in macrophages. These results demonstrate that TAK1 activity is the key to activated macrophage survival. Finally, in an in vivo setting, Tab1 deficiency impaired increase of peritoneal macrophages upon LPS challenge, suggesting that TAK1 complex regulation of macrophages may participate in in vivo macrophage homeostasis. Our results demonstrate that TAB1 and TAB2 are required for activated macrophages, making TAB1 and TAB2 effective targets to control inflammation by modulating macrophage survival.

  10. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

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    Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S

    2018-02-10

    We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

  11. Mcl-1 Ubiquitination: Unique Regulation of an Essential Survival Protein

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    Barbara Mojsa

    2014-05-01

    Full Text Available Mcl-1 is an anti-apoptotic protein of the Bcl-2 family that is essential for the survival of multiple cell lineages and that is highly amplified in human cancer. Under physiological conditions, Mcl-1 expression is tightly regulated at multiple levels, involving transcriptional, post-transcriptional and post-translational processes. Ubiquitination of Mcl-1, that targets it for proteasomal degradation, allows for rapid elimination of the protein and triggering of cell death, in response to various cellular events. In the last decade, a number of studies have elucidated different pathways controlling Mcl-1 ubiquitination and degradation. Four different E3 ubiquitin-ligases (e.g., Mule, SCFβ-TrCP, SCFFbw7 and Trim17 and one deubiquitinase (e.g., USP9X, that respectively mediate and oppose Mcl-1 ubiquitination, have been formerly identified. The interaction between Mule and Mcl-1 can be modulated by other Bcl-2 family proteins, while recognition of Mcl-1 by the other E3 ubiquitin-ligases and deubiquitinase is influenced by phosphorylation of specific residues in Mcl-1. The protein kinases and E3 ubiquitin-ligases that are involved in the regulation of Mcl-1 stability vary depending on the cellular context, highlighting the complexity and pivotal role of Mcl-1 regulation. In this review, we attempt to recapitulate progress in understanding Mcl-1 regulation by the ubiquitin-proteasome system.

  12. Predictive and comparative analysis of Ebolavirus proteins.

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    Cong, Qian; Pei, Jimin; Grishin, Nick V

    2015-01-01

    Ebolavirus is the pathogen for Ebola Hemorrhagic Fever (EHF). This disease exhibits a high fatality rate and has recently reached a historically epidemic proportion in West Africa. Out of the 5 known Ebolavirus species, only Reston ebolavirus has lost human pathogenicity, while retaining the ability to cause EHF in long-tailed macaque. Significant efforts have been spent to determine the three-dimensional (3D) structures of Ebolavirus proteins, to study their interaction with host proteins, and to identify the functional motifs in these viral proteins. Here, in light of these experimental results, we apply computational analysis to predict the 3D structures and functional sites for Ebolavirus protein domains with unknown structure, including a zinc-finger domain of VP30, the RNA-dependent RNA polymerase catalytic domain and a methyltransferase domain of protein L. In addition, we compare sequences of proteins that interact with Ebolavirus proteins from RESTV-resistant primates with those from RESTV-susceptible monkeys. The host proteins that interact with GP and VP35 show an elevated level of sequence divergence between the RESTV-resistant and RESTV-susceptible species, suggesting that they may be responsible for host specificity. Meanwhile, we detect variable positions in protein sequences that are likely associated with the loss of human pathogenicity in RESTV, map them onto the 3D structures and compare their positions to known functional sites. VP35 and VP30 are significantly enriched in these potential pathogenicity determinants and the clustering of such positions on the surfaces of VP35 and GP suggests possible uncharacterized interaction sites with host proteins that contribute to the virulence of Ebolavirus.

  13. Multivariate permutation test to compare survival curves for matched data

    National Research Council Canada - National Science Library

    Galimberti, Stefania; Valsecchi, Maria Grazia

    2013-01-01

    ... for the comparison of survival curves cannot be applied in this setting. We demonstrate the validity of the proposed method with simulations, and we illustrate its application to data from an observational study for the comparison of bone marrow transplantation and chemotherapy in the treatment of paediatric leukaemia. The use of the multivariate permutation testing approach is recommended in the highly stratified context of survival matched data, especially when the proportional hazards assumption does not hold.

  14. Comparative protein profiles of the Ambrosia plants.

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    Barton, Janice S; Schomacker, Rachel

    2017-06-01

    Ragweed pollen is primarily responsible for the hay fever allergies of sufferers throughout the world. A proteome study of three ragweed plants (Ambrosia artemisiifolia, Ambrosia trifida, and Ambrosia psilostachya) was undertaken to document and compare their protein profiles. Proteins extracted from the pollen of the three plants were subjected to one dimensional electrophoresis followed by tandem liquid chromatography-mass spectroscopy. Peptide sequence mapping permitted discovery of proteins not previously reported for all three plants and 45% of the identified proteins were shared by all three of them. Application of stringent criteria revealed not only a majority of known allergens for short ragweed but also allergens not previously reported for the other two plants. Additionally, potentially allergy inducing enolases are reported for the three plants. These results suggest that all three ragweed plants could contribute to the allergy malady. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Comparative footprinting of DNA-binding proteins.

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    Contreras-Moreira, Bruno; Collado-Vides, Julio

    2006-07-15

    Comparative modelling is a computational method used to tackle a variety of problems in molecular biology and biotechnology. Traditionally it has been applied to model the structure of proteins on their own or bound to small ligands, although more recently it has also been used to model protein-protein interfaces. This work is the first to systematically analyze whether comparative models of protein-DNA complexes could be built and be useful for predicting DNA binding sites. First, we describe the structural and evolutionary conservation of protein-DNA interfaces, and the limits they impose on modelling accuracy. Second, we find that side-chains from contacting residues can be reasonably modeled and therefore used to identify contacting nucleotides. Third, the DNASITE protocol is implemented and different parameters are benchmarked on a set of 85 regulators from Escherichia coli. Results show that comparative footprinting can make useful predictions based solely on structural data, depending primarily on the interface identity with respect to the template used. DNASITE code available on request from the authors.

  16. Expression of LDL receptor-related proteins (LRPs in common solid malignancies correlates with patient survival.

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    Steven L Gonias

    Full Text Available LDL receptor-related proteins (LRPs are transmembrane receptors involved in endocytosis, cell-signaling, and trafficking of other cellular proteins. Considerable work has focused on LRPs in the fields of vascular biology and neurobiology. How these receptors affect cancer progression in humans remains largely unknown. Herein, we mined provisional databases in The Cancer Genome Atlas (TCGA to compare expression of thirteen LRPs in ten common solid malignancies in patients. Our first goal was to determine the abundance of LRP mRNAs in each type of cancer. Our second goal was to determine whether expression of LRPs is associated with improved or worsened patient survival. In total, data from 4,629 patients were mined. In nine of ten cancers studied, the most abundantly expressed LRP was LRP1; however, a correlation between LRP1 mRNA expression and patient survival was observed only in bladder urothelial carcinoma. In this malignancy, high levels of LRP1 mRNA were associated with worsened patient survival. High levels of LDL receptor (LDLR mRNA were associated with decreased patient survival in pancreatic adenocarcinoma. High levels of LRP10 mRNA were associated with decreased patient survival in hepatocellular carcinoma, lung adenocarcinoma, and pancreatic adenocarcinoma. LRP2 was the only LRP for which high levels of mRNA expression correlated with improved patient survival. This correlation was observed in renal clear cell carcinoma. Insights into LRP gene expression in human cancers and their effects on patient survival should guide future research.

  17. Protein aggregation and protein instability govern familial amyotrophic lateral sclerosis patient survival.

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    Qi Wang

    2008-07-01

    Full Text Available The nature of the "toxic gain of function" that results from amyotrophic lateral sclerosis (ALS-, Parkinson-, and Alzheimer-related mutations is a matter of debate. As a result no adequate model of any neurodegenerative disease etiology exists. We demonstrate that two synergistic properties, namely, increased protein aggregation propensity (increased likelihood that an unfolded protein will aggregate and decreased protein stability (increased likelihood that a protein will unfold, are central to ALS etiology. Taken together these properties account for 69% of the variability in mutant Cu/Zn-superoxide-dismutase-linked familial ALS patient survival times. Aggregation is a concentration-dependent process, and spinal cord motor neurons have higher concentrations of Cu/Zn-superoxide dismutase than the surrounding cells. Protein aggregation therefore is expected to contribute to the selective vulnerability of motor neurons in familial ALS.

  18. Dietary proteins extend the survival of salmonella dublin in a gastric Acid environment

    DEFF Research Database (Denmark)

    Birk, Tina; Kristensen, Kim; Harboe, Anne

    2012-01-01

    The pH of the human stomach is dynamic and changes over time, depending on the composition of the food ingested and a number of host-related factors such as age. To evaluate the number of bacteria surviving the gastric acid barrier, we have developed a simple gastric acid model, in which we...... mimicked the dynamic pH changes in the human stomach. In the present study, model gastric fluid was set up to imitate pH dynamics in the stomachs of young and elderly people after ingestion of a standard meal. To model a serious foodborne pathogen, we followed the survival of Salmonella enterica serotype...... Dublin, and found that the addition of proteins such as pepsin, ovalbumin, and blended turkey meat to the simple gastric acid model significantly delayed pathogen inactivation compared with the control, for which no proteins were added. In contrast, no delay in inactivation was observed in the presence...

  19. E-Cadherin complex protein expression and survival in ovarian carcinoma.

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    Davidson, B; Gotlieb, W H; Ben-Baruch, G; Nesland, J M; Bryne, M; Goldberg, I; Kopolovic, J; Berner, A

    2000-12-01

    The aim of this study was to analyze the correlation between expression of E-cadherin complex proteins, epidermal growth factor receptor (EGFR), and c-erbB-2 and disease outcome in advanced-stage ovarian carcinomas. Sections from 75 primary ovarian carcinomas (=37) and metastatic lesions (=38) from 45 patients diagnosed with advanced-stage ovarian carcinoma (FIGO stage III-IV) were immunostained and evaluated for staining pattern, extent, and intensity. Patients were divided in two groups based on disease outcome. Long-term survivors (21 patients) and short-term survivors (24 patients) were defined using a double cutoff of 36 months for disease-free survival (DFS) and 60 months for overall survival (OS). Mean follow-up period was 70 months. The mean values for DFS and OS were 109 and 125 months for long-term survivors, as compared to 3 and 21 months for short-term survivors, respectively. Comparison of all primary and metastatic lesions showed upregulation of gamma-catenin protein expression in the latter (P = 0.05). When segregated according to disease outcome, the expression of all studied proteins, with the exception of EGFR, was more diffuse in tumors of short-term survivors. The presence of cytoplasmic staining for c-erbB-2 was associated with poor survival in the entire cohort (P = 0.007), as well as in primary tumors alone (P = 0.003), in survival analysis. Similar results were seen in the evaluation of primary tumors for gamma-catenin (P = 0.002). gamma-Catenin, and possibly c-erbB-2, are valid markers of poor survival in advanced-stage ovarian carcinoma. Copyright 2000 Academic Press.

  20. Incidence and survival from lung cancer in Greenland is comparable to survival in the Nordic countries

    DEFF Research Database (Denmark)

    Gelvan, Allan; Risum, Signe; Langer, Seppo W

    2015-01-01

    INTRODUCTION: Oncological treatment of lung cancer has been available in Greenland since 2004. We evaluated patient characteristics and survival rates for the first six years of local lung cancer treatment. METHODS: From September 2004 to August 2010, a total of 173 patients with lung cancer were...... referred to treatment at Queen Ingrid's Hospital. On 1 February 2014, treatment results, survival, and prognostic variables were analysed. RESULTS: The mean age at diagnosis was 63 years. Non-small cell lung cancer (NSCLC) was diagnosed in 145 patients (84%); 56% had squamous cell carcinoma, 34% had...... adenocarcinoma, 2% had large cell carcinoma and 8% had NSCLC not otherwise specified (NOS). In all, 28 (16%) had small cell lung cancer. A total of 142 patients (82%) received treatment; 20 underwent surgery (ten stage Ib, one stage IIa, five stage IIb, four stage IIIa); palliative chemotherapy was given to 122...

  1. Evaluation of serum biochemical marker concentrations and survival time in dogs with protein-losing enteropathy.

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    Equilino, Mirjam; Théodoloz, Vincent; Gorgas, Daniela; Doherr, Marcus G; Heilmann, Romy M; Suchodolski, Jan S; Steiner, Jörg M; Burgener Dvm, Iwan A

    2015-01-01

    To evaluate serum concentrations of biochemical markers and survival time in dogs with protein-losing enteropathy (PLE). Prospective study. 29 dogs with PLE and 18 dogs with food-responsive diarrhea (FRD). Data regarding serum concentrations of various biochemical markers at the initial evaluation were available for 18 of the 29 dogs with PLE and compared with findings for dogs with FRD. Correlations between biochemical marker concentrations and survival time (interval between time of initial evaluation and death or euthanasia) for dogs with PLE were evaluated. Serum C-reactive protein concentration was high in 13 of 18 dogs with PLE and in 2 of 18 dogs with FRD. Serum concentration of canine pancreatic lipase immunoreactivity was high in 3 dogs with PLE but within the reference interval in all dogs with FRD. Serum α1-proteinase inhibitor concentration was less than the lower reference limit in 9 dogs with PLE and 1 dog with FRD. Compared with findings in dogs with FRD, values of those 3 variables in dogs with PLE were significantly different. Serum calprotectin (measured by radioimmunoassay and ELISA) and S100A12 concentrations were high but did not differ significantly between groups. Seventeen of the 29 dogs with PLE were euthanized owing to this disease; median survival time was 67 days (range, 2 to 2,551 days). Serum C-reactive protein, canine pancreatic lipase immunoreactivity, and α1-proteinase inhibitor concentrations differed significantly between dogs with PLE and FRD. Most initial biomarker concentrations were not predictive of survival time in dogs with PLE.

  2. Patient Survival and Costs on Moderately Restricted Low-Protein Diets in Advanced CKD: Equivalent Survival at Lower Costs?

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    Giorgina Barbara Piccoli

    2016-11-01

    Full Text Available The indications for delaying the start of dialysis have revived interest in low-protein diets (LPDs. In this observational prospective study, we enrolled all patients with chronic kidney disease (CKD who followed a moderately restricted LPD in 2007–2015 in a nephrology unit in Italy: 449 patients, 847 years of observation. At the start of the diet, the median glomerular filtration rate (GFR was 20 mL/min, the median age was 70, the median Charlson Index was 7. Standardized mortality rates for the “on-diet” population were significantly lower than for patients on dialysis (United States Renal Data System (USRDS: 0.44 (0.36–0.54; Italian Dialysis Registry: 0.73 (0.59–0.88; French Dialysis Registry 0.70 (0.57–0.85. Considering only the follow-up at low GFR (≤15 mL/min, survival remained significantly higher than in the USRDS, and was equivalent to the Italian and French registries, with an advantage in younger patients. Below the e-GFR of 15 mL/min, 50% of the patients reached a dialysis-free follow-up of ≥2 years; 25% have been dialysis-free for five years. Considering an average yearly cost of about 50,000 Euros for dialysis and 1200 Euros for the diet, and different hypotheses of “spared” dialysis years, treating 100 patients on a moderately restricted LPD would allow saving one to four million Euros. Therefore, our study suggests that in patients with advanced CKD, moderately restricted LPDs may allow prolonging dialysis-free follow-up with comparable survival to dialysis at a lower cost.

  3. Role of PPE18 protein in intracellular survival and pathogenicity of Mycobacterium tuberculosis in mice.

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    Khalid Hussain Bhat

    Full Text Available BACKGROUND: Ever since its discovery the mycobacterial proline-proline-glutamic acid (PPE family of proteins has generated a huge amount of interest. Understanding the role of these proteins in the pathogenesis of Mycobacterium tuberculosis (Mtb is important. We have demonstrated earlier that the PPE18 protein of Mtb induces IL-10 production in macrophages with subsequent downregulation of pro-inflammatory cytokines like IL-12 and TNF-α and favors a T-helper (Th 2-type of immune response. METHODOLOGY/PRINCIPAL FINDINGS: Using a ppe18 genetic knock-out Mtb strain, we have now carried out infection studies in mice to understand the role of PPE18 in Mtb virulence. The studies reveal that lack of PPE18 leads to attenuation of Mtb in vivo. Mice infected with the ppe18 deleted strain have reduced infection burden in lung, liver and spleen and have better survival rates compared to mice infected with the wild-type Mtb strain. CONCLUSIONS/SIGNIFICANCE: Taken together our data suggest that PPE18 could be a crucial virulence factor for intracellular survival of Mtb.

  4. The prohibitin protein complex promotes mitochondrial stabilization and cell survival in hematologic malignancies

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    Ross, Jeremy A.; Robles-Escajeda, Elisa; Oaxaca, Derrick M.; Padilla, Diana L.; Kirken, Robert A.

    2017-01-01

    Prohibitins (PHB1 and PHB2) have been proposed to play important roles in cancer development and progression, however their oncogenic mechanism of action has not been fully elucidated. Previously, we showed that the PHB1 and PHB2 protein complex is required for mitochondrial homeostasis and survival of normal human lymphocytes. In this study, novel evidence is provided that indicates mitochondrial prohibitins are overexpressed in hematologic tumor cells and promote cell survival under conditions of oxidative stress. Immunofluorescent confocal microscopy revealed both proteins to be primarily confined to mitochondria in primary patient lymphoid and myeloid tumor cells and tumor cell lines, including Kit225 cells. Subsequently, siRNA-mediated knockdown of PHB1 and PHB2 in Kit225 cells significantly enhanced sensitivity to H2O2-induced cell death, suggesting a protective or anti-apoptotic function in hematologic malignancies. Indeed, PHB1 and PHB2 protein levels were significantly higher in tumor cells isolated from leukemia and lymphoma patients compared to PBMCs from healthy donors. These findings suggest that PHB1 and PHB2 are upregulated during tumorigenesis to maintain mitochondrial integrity and therefore may serve as novel biomarkers and molecular targets for therapeutic intervention in certain types of hematologic malignancies. PMID:29029444

  5. Comparing Temperature Effects on E. Coli, Salmonella, and Enterococcus Survival in Surface Waters

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    The objective of this study was to compare dependency of survival rates on temperature for indicator organisms E. coli and Enterococcus and the pathogen Salmonella in surface waters. A database of 86 survival datasets from peer-reviewed papers on inactivation of E. coli, Salmonel...

  6. Choline kinase alpha and hexokinase-2 protein expression in hepatocellular carcinoma: association with survival.

    Directory of Open Access Journals (Sweden)

    Sandi A Kwee

    Full Text Available PURPOSE: Hexokinase-2 (HK2 and more recently choline kinase alpha (CKA expression has been correlated with clinical outcomes in several major cancers. This study examines the protein expression of HK2 and CKA in hepatocellular carcinoma (HCC in association with patient survival and other clinicopathologic parameters. METHODS: Immunohistochemical analysis for HK2 and CKA expression was performed on a tissue microarray of 157 HCC tumor samples. Results were analyzed in relation to clinicopathologic data from Surveillance, Epidemiology, and End-Results Program registries. Mortality rates were assessed by Kaplan-Meier estimates and compared using log-rank tests. Predictors of overall survival were assessed using proportional hazards regression. RESULTS: Immunohistochemical expression of HK2 and CKA was detected in 71 (45% and 55 (35% tumor samples, respectively. Differences in tumor HK2 expression were associated with tumor grade (p = 0.008 and cancer stage (p = 0.001, while CKA expression differed significantly only across cancer stage (p = 0.048. Increased mortality was associated with tumor HK2 expression (p = 0.003 as well as CKA expression (p = 0.03 with hazard ratios of 1.86 (95% confidence interval (CI 1.23-2.83 and 1.59 (95% CI 1.04-2.41, respectively. Similar effects on overall survival were noted in a subset analysis of early stage (I and II HCC. Tumor HK2 expression, but not CKA expression, remained a significant predictor of survival in multivariable analyses. CONCLUSION: HK2 and CKA expression may have biologic and prognostic significance in HCC, with tumor HK2 expression being a potential independent predictor of survival.

  7. Protein kinase G1 α overexpression increases stem cell survival and cardiac function after myocardial infarction.

    Directory of Open Access Journals (Sweden)

    Linlin Wang

    Full Text Available We hypothesized that overexpression of cGMP-dependent protein kinase type 1α (PKG1α could mimic the effect of tadalafil on the survival of bone marrow derived mesenchymal stem cells (MSCs contributing to regeneration of the ischemic heart.MSCs from male rats were transduced with adenoviral vector encoding for PKG1α ((PKG1αMSCs.Controls included native MSCs ((NatMSCs and MSCs transduced with an empty vector ((NullMSCs. PKG1α activity was increased approximately 20, 5 and 16 fold respectively in (PKG1αMSCs. (PKG1αMSCs showed improved survival under oxygen and glucose deprivation (OGD which was evidenced by lower LDH release, caspase-3/7 activity and number of positive TUNEL cells. Anti-apoptotic proteins pAkt, pGSK3β, and Bcl-2 were significantly increased in (PKG1αMSCs compared to (NatMSCs and (NullMSCs. Higher release of multiple prosurvival and angiogenic factors such as HGF, bFGF, SDF-1 and Ang-1 was observed in (PKG1αMSCs before and after OGD. In a female rat model of acute myocardial infarction, (PKG1αMSCs group showed higher survival compared with (NullMSCs group at 3 and 7 days after transplantation as determined by TUNEL staining and sry-gene quantitation by real-time PCR. Increased anti-apoptotic proteins and paracrine factors in vitro were also identified. Immunostaining for cardiac troponin I combined with GFP showed increased myogenic differentiation of (PKG1αMSCs. At 4 weeks after transplantation, compared to DMEM group and (NullMSCs group, (PKG1αMSCs group showed increased blood vessel density in infarct and peri-infarct areas (62.5±7.7; 68.8±7.3 per microscopic view, p<0.05 and attenuated infarct size (27.2±2.5%, p<0.01. Heart function indices including ejection fraction (52.1±2.2%, p<0.01 and fractional shortening (24.8%±1.3%, p<0.01 were improved significantly in (PKG1αMSCs group.Overexpression of PKG1α transgene could be a powerful approach to improve MSCs survival and their angiomyogenic potential in the

  8. Survival

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — These data provide information on the survival of California red-legged frogs in a unique ecosystem to better conserve this threatened species while restoring...

  9. Antifreeze proteins enable plants to survive in freezing conditions

    Indian Academy of Sciences (India)

    Overwintering plants secrete antifreeze proteins (AFPs) to provide freezing tolerance. These proteins bind to and inhibit the growth of ice crystals that are formed in the apoplast during subzero temperatures. Antifreeze activity has been detected in more than 60 plants and AFPs have been purified from 15 of these, including ...

  10. Comparative interactomics for virus-human protein-protein interactions: DNA viruses versus RNA viruses.

    Science.gov (United States)

    Durmuş, Saliha; Ülgen, Kutlu Ö

    2017-01-01

    Viruses are obligatory intracellular pathogens and completely depend on their hosts for survival and reproduction. The strategies adopted by viruses to exploit host cell processes and to evade host immune systems during infections may differ largely with the type of the viral genetic material. An improved understanding of these viral infection mechanisms is only possible through a better understanding of the pathogen-host interactions (PHIs) that enable viruses to enter into the host cells and manipulate the cellular mechanisms to their own advantage. Experimentally-verified protein-protein interaction (PPI) data of pathogen-host systems only became available at large scale within the last decade. In this study, we comparatively analyzed the current PHI networks belonging to DNA and RNA viruses and their human host, to get insights into the infection strategies used by these viral groups. We investigated the functional properties of human proteins in the PHI networks, to observe and compare the attack strategies of DNA and RNA viruses. We observed that DNA viruses are able to attack both human cellular and metabolic processes simultaneously during infections. On the other hand, RNA viruses preferentially interact with human proteins functioning in specific cellular processes as well as in intracellular transport and localization within the cell. Observing virus-targeted human proteins, we propose heterogeneous nuclear ribonucleoproteins and transporter proteins as potential antiviral therapeutic targets. The observed common and specific infection mechanisms in terms of viral strategies to attack human proteins may provide crucial information for further design of broad and specific next-generation antiviral therapeutics.

  11. Protein kinase activity of phosphoinositide 3-kinase regulates cytokine-dependent cell survival.

    Directory of Open Access Journals (Sweden)

    Daniel Thomas

    Full Text Available The dual specificity protein/lipid kinase, phosphoinositide 3-kinase (PI3K, promotes growth factor-mediated cell survival and is frequently deregulated in cancer. However, in contrast to canonical lipid-kinase functions, the role of PI3K protein kinase activity in regulating cell survival is unknown. We have employed a novel approach to purify and pharmacologically profile protein kinases from primary human acute myeloid leukemia (AML cells that phosphorylate serine residues in the cytoplasmic portion of cytokine receptors to promote hemopoietic cell survival. We have isolated a kinase activity that is able to directly phosphorylate Ser585 in the cytoplasmic domain of the interleukin 3 (IL-3 and granulocyte macrophage colony stimulating factor (GM-CSF receptors and shown it to be PI3K. Physiological concentrations of cytokine in the picomolar range were sufficient for activating the protein kinase activity of PI3K leading to Ser585 phosphorylation and hemopoietic cell survival but did not activate PI3K lipid kinase signaling or promote proliferation. Blockade of PI3K lipid signaling by expression of the pleckstrin homology of Akt1 had no significant impact on the ability of picomolar concentrations of cytokine to promote hemopoietic cell survival. Furthermore, inducible expression of a mutant form of PI3K that is defective in lipid kinase activity but retains protein kinase activity was able to promote Ser585 phosphorylation and hemopoietic cell survival in the absence of cytokine. Blockade of p110α by RNA interference or multiple independent PI3K inhibitors not only blocked Ser585 phosphorylation in cytokine-dependent cells and primary human AML blasts, but also resulted in a block in survival signaling and cell death. Our findings demonstrate a new role for the protein kinase activity of PI3K in phosphorylating the cytoplasmic tail of the GM-CSF and IL-3 receptors to selectively regulate cell survival highlighting the importance of targeting

  12. Phosphatidylinositol transfer proteins in cell survival and apoptosis

    NARCIS (Netherlands)

    Schenning, M.

    2007-01-01

    Mouse fibroblast cells overexpressing phosphatidylinositol transfer protein alpha [PI-TPalpha; sense PI-TPalpha (SPIalpha) cells] show a significantly increased rate of proliferation and an extreme resistance toward ultraviolet- or tumor necrosis factor-alpha-induced apoptosis. The fact that the

  13. A novel cell immunoassay to measure survival of motor neurons protein in blood cells

    Directory of Open Access Journals (Sweden)

    Fischbeck Kenneth H

    2006-02-01

    Full Text Available Abstract Background The motor neuron degenerative disease spinal muscular atrophy (SMA is the leading genetic cause of infant mortality and is caused by mutations in the survival of motor neurons (SMN gene that reduce the expression levels of the SMN protein. A major goal of current therapeutic approaches is to increase SMN levels in SMA patients. The purpose of this study was to develop a reliable assay to measure SMN protein levels from peripheral blood samples. Methods We developed a novel cell immunoassay to quantitatively measure SMN levels from peripheral blood mononuclear cells (PBMCs using a single anti-SMN antibody. Results SMN levels determined by the cell immunoassay are comparable to levels determined by Western blot, but in contrast, the immunoassay does not involve cell lysis, requires a small amount of patient material, and can be done on a large number of samples simultaneously. SMN levels from PBMCs are not influenced by cell type heterogeneity. Conclusion SMN levels measured from total PBMCs provide an important snapshot of SMN protein expression, which should be a useful aid in SMA diagnosis, and a surrogate marker of efficacy of treatment in SMA clinical trials.

  14. Heat shock protein expression in relation to reproductive cycle in land snails: Implications for survival.

    Science.gov (United States)

    Mizrahi, Tal; Heller, Joseph; Goldenberg, Shoshana; Arad, Zeev

    2011-10-01

    Land snails are subject to daily and seasonal variations in temperature and in water availability and use heat shock proteins (HSPs) as part of their survival strategy. We tested whether the reproductive cycle of land snails affects the endogenous levels of HSPs, and their involvement in the reproductive process. We examined HSP levels in the foot tissue of two Sphincterochila species, S. cariosa and S. zonata, before and after laying eggs, and analyzed the albumen gland (reproductive organ) of both species and eggs of S. cariosa for the presence and quantity of various HSPs. Our study shows reduction in the expression level of Hsp70 isoforms and Hsp90 in S. zonata foot and of Hsp74 in S. cariosa foot during the period preceding egg laying compared to the post-reproductive stage. Hsp70 isoforms and Hsp25 were highly expressed in both large albumen glands and in freshly laid eggs of S. cariosa, whereas large albumen glands of S. zonata expressed mainly Hsp70 isoforms. We conclude that a trade-off between survival and fertility is responsible for the expression level of HSPs in the foot tissue of Sphincterochila snails. Our study shows that HSPs are involved in the reproductive process. We propose that parental provision of HSPs may be part of a "be prepared" strategy of Sphincterochila snails, and that HSPs may play important roles in the survival strategy of land snails during the early life stages. Our observations also highlight the importance of the reproductive status in study of whole organisms, especially when assessing the HSP response to stress. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. Interactive effects of selenium, methionine, and dietary protein on survival, growth, and physiology in mallard ducklings

    Science.gov (United States)

    Hoffman, D.J.; Sanderson, C.J.; LeCaptain, L.J.; Cromartie, E.; Pendleton, G.W.

    1992-01-01

    Concentrations of over 100 ppm (100 mg/kg) selenium (Se) have been found in aquatic food chains associated with irrigation drainwater. Both quantity and composition of dietary protein for wild ducklings may vary in selenium-contaminated environments. Day-old mallard (Anas platyrhynchos) ducklings received one of the following diets containing 22% protein: unsupplemented (controls), 15 ppm Se (as selenomethionine), 60 ppm Se, methionine supplemented, 15 ppm Se with methionine supplement, or 60 ppm Se with methionine supplement. In a second concurrent experiment the above sequence was repeated with a protein-restricted (11%) but isocaloric diet. In a third concurrent experiment all ducklings received 44% protein with 0, 15, or 60 ppm Se added. After 4 weeks, blood and tissue samples were collected for biochemical and histological examination. With 22% protein and 60 ppm Se in the diet, duckling survival and growth was reduced and histopathological lesions of the liver occurred. Antagonistic interactive effects occurred between supplementary methionine and Se, including complete to partial alleviation of the following Se effects by methionine: mortality, hepatic lesions, and altered glutathione and thiol status. With 11% protein, growth of controls was less than that with 22% protein, Se (60 ppm) caused 100% mortality, and methionine supplementation, although protective afforded less protection than it did with 22% protein. With 44% protein, ducklings experienced physiological stress, and Se was more toxic than with methionine-supplemented 22% protein. These findings suggest the potential for antagonistic effects of Se, methionine, and protein on duckling survival and physiology.

  16. Evolution versus "intelligent design": comparing the topology of protein-protein interaction networks to the Internet.

    Science.gov (United States)

    Yang, Q; Siganos, G; Faloutsos, M; Lonardi, S

    2006-01-01

    Recent research efforts have made available genome-wide, high-throughput protein-protein interaction (PPI) maps for several model organisms. This has enabled the systematic analysis of PPI networks, which has become one of the primary challenges for the system biology community. In this study, we attempt to understand better the topological structure of PPI networks by comparing them against man-made communication networks, and more specifically, the Internet. Our comparative study is based on a comprehensive set of graph metrics. Our results exhibit an interesting dichotomy. On the one hand, both networks share several macroscopic properties such as scale-free and small-world properties. On the other hand, the two networks exhibit significant topological differences, such as the cliqueishness of the highest degree nodes. We attribute these differences to the distinct design principles and constraints that both networks are assumed to satisfy. We speculate that the evolutionary constraints that favor the survivability and diversification are behind the building process of PPI networks, whereas the leading force in shaping the Internet topology is a decentralized optimization process geared towards efficient node communication.

  17. Effects of protein kinase C activators and staurosporine on protein kinase activity, cell survival, and proliferation in Tetrahymena thermophila

    DEFF Research Database (Denmark)

    Straarup, EM; Schousboe, P; Hansen, HQ

    1997-01-01

    Autocrine factors prevent cell death in the ciliate Tetrahymena thermophila, a unicellular eukaryote, in a chemically defined medium. At certain growth conditions these factors are released at a sufficient concentration by > 500 cells ml-1 to support cell survival and proliferation. The protein k...

  18. Interactive effects of arsenate, selenium, and dietary protein on survival, growth, and physiology in mallard ducklings

    Science.gov (United States)

    Hoffman, D.J.; Sanderson, C.J.; LeCaptain, L.J.; Cromartie, E.; Pendleton, G.W.

    1992-01-01

    High concentrations of arsenic (As) and selenium (Se) have been found in aquatic food chains associated with irrigation drainwater. Total biomass of invertebrates, a maJor source of protein for wild ducklings, may vary in environments that are contaminated with selenium. Dayold mallard (Anas platyrhynchos) ducklings received an untreated diet (controls) containing 22% protein or diets containing 15 ppm Se (as selenomethionine), 60 ppm Se, 200 ppm As (as sodium arsenate), 15 ppm Se with 200 ppm As, or 60 ppm Se with 200 ppm As. In a concurrent experiment, the same sequence was repeated with a proteinrestricted (7%) but isocaloric diet. After 4 weeks, blood and tissue samples were collected for biochemical and histological examination. With 22% protein and 60 ppm Se in the diet, duckling survival and growth was reduced and livers had histopathological lesions. Arsenic alone caused some reduction in growth. Antagonistic interactive effects occurred between As and Se, including complete to partial alleviation of the following Se effects: mortality, impaired growth, hepatic lesions and lipid peroxidation, and altered glutathione and thiol status. With 7% protein, survival and growth of controls was less than that with 22% protein, Se (60 ppm) caused 100% mortality, and As (200 ppm) caused mortality, decreased growth, and liver histopathology. These findings suggest the potential for antagonistic effects of Se and As on duckling survival, growth, and physiology with adequate dietary protein but more severe toxicological effects when dietary protein is diminished.

  19. Renal cell carcinoma in end-stage renal disease: Multi-institutional comparative analysis of survival.

    Science.gov (United States)

    Song, Cheryn; Hong, Sung Hoo; Chung, Jin Soo; Byun, Seok Soo; Kwak, Cheol; Jeong, Chang Wook; Seo, Seong Il; Jeon, Hwang Gyun; Seo, Ill Young

    2016-06-01

    To describe the clinical features of renal cell carcinoma arising in end-stage renal disease and to compare survival outcomes after definitive treatment with non-end-stage renal disease renal cell carcinoma. Data of 181 consecutive patients with end-stage renal disease renal cell carcinoma who had received surgical treatment between 1995 and 2011 at seven institutions were reviewed. Data of 362 non-end-stage renal disease renal cell carcinoma patients matched for clinicopathological parameters who received surgery at Asan Medical Center during the same study period were also reviewed. The two study groups were compared with respect to recurrence-free, cancer-specific, and overall survival by Kaplan-Meier analysis and Cox proportional hazards method. Mean follow up was 40 ± 34.2 months after surgery. Median tumor size was 2.5 cm (interquartile range 1.5-4.5), and pathological tumor stage was T1 in 78%, T2 in 7.1% and T3 and higher in 14.9%. Tumor histological type was clear cell in 63%, papillary in 17%, chromophobe in 5%, clear cell papillary in 2.8% and acquired cystic disease-related in 6.1%. Compared with the controls, the stage-specific 5-year recurrence-free survival was similar (87.6 vs 88.5%), but cancer-specific and overall survival was significantly lower. On multivariate analysis, end-stage renal disease renal cell carcinoma was not a predictor for recurrence-free survival, but a significant predictor for cancer-specific (hazard ratio 4.07, 95% confidence interval 2.08-7.94) and overall survival (hazard ratio 3.13, 95% confidence interval 1.66-5.96). End-stage renal disease renal cell carcinoma seems to have comparable stage-specific recurrence-free, but poorer cancer-specific and overall survival compared with non-end-stage renal disease renal cell carcinoma. As patients with end-stage renal disease are a high-risk population for renal cell carcinoma, routine radiographic screening to improve survival outcomes should be further investigated. © 2016

  20. Club cell secretory protein improves survival in a murine obliterative bronchiolitis model.

    Science.gov (United States)

    Wendt, Christine; Tram, Kevin; Price, Andrew; England, Kristen; Stiehm, Andrew; Panoskaltsis-Mortari, Angela

    2013-11-01

    Club cell secretory protein (CCSP) is an indirect phospholipase A2 inhibitor with some immunosuppressive and antiproliferative properties that is expressed in bronchiolar Club cells. In our murine bone marrow transplant (BMT) model of obliterative bronchiolitis (OB), CCSP is diminished; however, its role is unknown. To determine the role of CCSP, B6 wild-type (WT) or CCSP-deficient (CCSP(-/-)) mice were lethally conditioned and given allogeneic bone marrow with a sublethal dose of allogeneic splenic T cells to induce OB. We found that CCSP(-/-) mice demonstrated a higher mortality following BMT-induced OB compared with WT mice. Mice were analyzed 60 days post-BMT for protein expression, pulmonary function, and histology. CCSP levels were reduced in WT mice with BMT-induced OB, and lower levels correlated to decreased lung compliance. CCSP(-/-) had a higher degree of injury and fibrosis as measured by hydroxy proline, along with an increased lung resistance and the inflammatory markers, leukotriene B4 and CXCL1. Replacement with recombinant intravenous CCSP partially reversed the weight loss and improved survival in the CCSP(-/-) mice. In addition, CCSP replacement improved histology and decreased inflammatory cells and markers. These findings indicate that CCSP has a regulatory role in OB and may have potential as a preventive therapy.

  1. SCPC: a method to structurally compare protein complexes.

    Science.gov (United States)

    Koike, Ryotaro; Ota, Motonori

    2012-02-01

    Protein-protein interactions play vital functional roles in various biological phenomena. Physical contacts between proteins have been revealed using experimental approaches that have solved the structures of protein complexes at atomic resolution. To examine the huge number of protein complexes available in the Protein Data Bank, an efficient automated method that compares protein complexes is required. We have developed Structural Comparison of Protein Complexes (SCPC), a novel method to structurally compare protein complexes. SCPC compares the spatial arrangements of subunits in a complex with those in another complex using secondary structure elements. Similar substructures are detected in two protein complexes and the similarity is scored. SCPC was applied to dimers, homo-oligomers and haemoglobins. SCPC properly estimated structural similarities between the dimers examined as well as an existing method, MM-align. Conserved substructures were detected in a homo-tetramer and a homo-hexamer composed of homologous proteins. Classification of quaternary structures of haemoglobins using SCPC was consistent with the conventional classification. The results demonstrate that SCPC is a valuable tool to investigate the structures of protein complexes. SCPC is available at http://idp1.force.cs.is.nagoya-u.ac.jp/scpc/. rkoike@is.nagoya-u.ac.jp Supplementary data are available at Bioinformatics online.

  2. Comparative Evaluation of Animal with Plant Protein Intake in ...

    African Journals Online (AJOL)

    Comparative Evaluation of Animal with Plant Protein Intake in Northern Adamawa State of Nigeria. HI Kubkomawa, R Midiga, UO Helen, B Williams, F Timon. Abstract. The study was conducted to compare the preference, acceptability and consumption of animal and plant protein intakes in Adamawa State, northern eastern, ...

  3. Comparing temperature effects on Escherichia coli, Salmonella, and Enterococcus survival in surface waters.

    Science.gov (United States)

    Pachepsky, Y A; Blaustein, R A; Whelan, G; Shelton, D R

    2014-09-01

    The objective of this study was to compare dependency of survival rates on temperature for indicator organisms Escherichia coli and Enterococcus and the pathogen Salmonella in surface waters. A database of 86 survival datasets from peer-reviewed papers on inactivation of E. coli, Salmonella and Enterococcus in marine waters and of E. coli and Salmonella in lake waters was assembled. The Q10 model was used to express temperature effect on survival rates obtained from linear sections of semi-logarithmic survival graphs. Available data were insufficient to establish differences in survival rates and temperature dependencies for marine waters where values of Q10  = 3 and a survival rate of 0·7 day(-1) could be applied. The Q10 values in lake waters were substantially lower in marine waters, and Salmonella inactivation in lake water was, on average, twice as fast as E. coli; data on E. coli substantially outnumber data on Enterococcus and Salmonella. The relative increase in inactivation with increase in temperature is higher in marine waters than lake water, and differences in inactivation between Salmonella and E. coli at a given temperature were significant in lake water but not in marine waters. Microbiological quality of surface waters is of paramount importance for public health. The novelty of this work is using a large compendium of published data to develop the first comparison of temperature effects on survival of the pathogen Salmonella and water quality indicator micro-organisms Escherichia coli and Enterococcus in natural waters. The existing relatively large body of knowledge on E. coli survival appears to be useful to assess the effect of temperature on survival of Salmonella. Moreover, results of this work constitute an essential input in models to support environmental management decisions on the use of surface water sources in agriculture, aquaculture and recreation. © Published 2014. This article is a U.S. Government work and is in the

  4. ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.

    Directory of Open Access Journals (Sweden)

    John A Capra

    Full Text Available The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight into the cellular functions and interactions of proteins, such comparative phylogenetic analyses are rarely performed, because they require custom algorithms. We developed ProteinHistorian to make tools for performing analyses of protein origins widely available. Given a list of proteins of interest, ProteinHistorian estimates the phylogenetic age of each protein, quantifies enrichment for proteins of specific ages, and compares variation in protein age with other protein attributes. ProteinHistorian allows flexibility in the definition of protein age by including several algorithms for estimating ages from different databases of evolutionary relationships. We illustrate the use of ProteinHistorian with three example analyses. First, we demonstrate that proteins with high expression in human, compared to chimpanzee and rhesus macaque, are significantly younger than those with human-specific low expression. Next, we show that human proteins with annotated regulatory functions are significantly younger than proteins with catalytic functions. Finally, we compare protein length and age in many eukaryotic species and, as expected from previous studies, find a positive, though often weak, correlation between protein age and length. ProteinHistorian is available through a web server with an intuitive interface and as a set of command line tools; this allows biologists and bioinformaticians alike to integrate these approaches into their analysis pipelines. ProteinHistorian's modular, extensible design facilitates the integration of new datasets and algorithms. The ProteinHistorian web server, source code, and pre-computed ages for 32 eukaryotic genomes are

  5. Escherichia coli MazF leads to the simultaneous selective synthesis of both "death proteins" and "survival proteins".

    Directory of Open Access Journals (Sweden)

    Shahar Amitai

    2009-03-01

    Full Text Available The Escherichia coli mazEF module is one of the most thoroughly studied toxin-antitoxin systems. mazF encodes a stable toxin, MazF, and mazE encodes a labile antitoxin, MazE, which prevents the lethal effect of MazF. MazF is an endoribonuclease that leads to the inhibition of protein synthesis by cleaving mRNAs at ACA sequences. Here, using 2D-gels, we show that in E. coli, although MazF induction leads to the inhibition of the synthesis of most proteins, the synthesis of an exclusive group of proteins, mostly smaller than about 20 kDa, is still permitted. We identified some of those small proteins by mass spectrometry. By deleting the genes encoding those proteins from the E. coli chromosome, we showed that they were required for the death of most of the cellular population. Under the same experimental conditions, which induce mazEF-mediated cell death, other such proteins were found to be required for the survival of a small sub-population of cells. Thus, MazF appears to be a regulator that induces downstream pathways leading to death of most of the population and the continued survival of a small sub-population, which will likely become the nucleus of a new population when growth conditions become less stressful.

  6. Interactive effects of boron, selenium, and dietary protein on survival, growth and physiology in mallard ducklings

    Science.gov (United States)

    Hoffman, D.J.; Sanderson, C.J.; LeCaptain, L.J.; Cromartie, E.; Pendleton, G.W.

    1991-01-01

    High concentrations of boron (B) and selenium (Se) have been found in aquatic food chains associated with irrigation drainwater. Total biomass of invertebrates, a maJor source of protein for wild ducklings, is sometimes diminished in agricultural drainwater ponds contaminated with Se and B. Dayold mallard (Anas platyrhynchos) ducklings received an untreated diet (controls) containing 22% protein or diets containing 15 ppm (microgram/g) Se (as selenomethionine), 60 ppm Se, 1,000 ppm B (as boric acid), 15 ppm Se with 1,000 ppm B, or 60 ppm Se with 1,000 ppm B. In a concurrent experiment, the above sequence was repeated with a proteinrestricted (7%) but isocaloric diet. After four weeks, blood and tissue samples were collected for biochemical and histological examination. With 22% protein and 60 ppm Se in the diet, duckling survival and growth was reduced and histopathological lesions of the liver occurred. Boron alone caused some reduction in growth. Several interactive effects occurred between B and Se, including further reduction in growth, and increases in plasma glutathione reductase activity, hematocrit, hemoglobin and plasma protein concentrations. With 7% protein, the growth of controls was less than that with 22% protein, 60 ppm Se caused 100% mortality, and growth effects of 15 ppm Se and 1,000 ppm B alone were more pronounced than with 22% protein. Selenium accumulation increased in the liver with 7% protein. Interactive effects were greater for Se and B with 7% protein than with 22% protein and included significant mortality and enhanced accumulation of Se in the liver. These findings suggest the potential for more severe toxicological effects of Se and B independently and interactively on duckling survival and development when dietary protein is diminished.

  7. Comparable cell survival between high dose rate flattening filter free and conventional dose rate irradiation.

    Science.gov (United States)

    Verbakel, Wilko F A R; van den Berg, Jaap; Slotman, Ben J; Sminia, Peter

    2013-04-01

    Investigation of clonogenic cell survival and cell proliferation following single dose and fractionated delivery of high dose rate flattening filter free (FFF) irradiation compared to conventional dose rates. The human astrocytoma D384, glioma T98 and lung carcinoma SW1573 cell lines were irradiated using either a single dose (0-12 Gy) or a fractionated protocol of 5 daily fractions of 2 Gy (D384) or 3 Gy (SW1573). Cells were irradiated inside a phantom using fixed gantry beams of a linear accelerator. A sliding window technique created homogeneous dose distributions over the surface of the cell cultures. Irradiations using standard beams (6 MV, 600 MU/min.) and high dose rate FFF beams (10 MV, 2400 MU/min.) were compared. Cell survival was determined by clonogenic assay. In the fractionated irradiation set-up, the number of clonogenic cells was estimated by including tumor cell proliferation during the overall treatment time in the analysis. All cell lines showed equal cell survival following irradiation using either the FFF beams or conventional flattened (FF) beams. This was observed after single dose exposure (0-12 Gy) as well as after fractionated irradiation (p = 0.08 for D384 and 0.20 for SW1373 cell lines). FFF irradiation with a dose rate of 2400 MU/min and four times higher dose per pulse compared to irradiation with FF beams did not change cell survival for three human cancer cell lines up to a fraction dose of 12 Gy compared to irradiation using FF beams.

  8. Differential effect of protein-bound polysaccharide (PSK) on survival of experimental murine tumors.

    Science.gov (United States)

    Algarra, I; Collado, A; Garcia Lora, A; Garrido, F

    1999-03-01

    The effect of protein-bound polysaccharide (PSK) on the survival of BALB/c and C57BL/6 mice after intravenous injections of syngeneic murine sarcomas (GR9.B9 and Meth-A), LSTRA lymphoma and B16 melanoma cells was studied. Pretreatment of mice with PSK significantly increased survival after the injection of either type of sarcoma cells, although the effect was attenuated when high numbers of cells were injected. Survival was not modified significantly in LSTRA lymphoma or B16 melanoma. Mice pretreated with anti-asialo GMI serum showed significantly decreased survival from all tumors in comparison with untreated mice injected with tumors, regardless of cell dose used. We observed an inverse correlation between H-2 antigen expression and in vitro NK sensitivity of tumor cells from all lines except B16 melanoma cells. These results clearly suggest that pretreatment of mice with PSK prolongs survival and inhibits metastasis formation in mice injected with sarcoma cells, being this effect highly selective, since survival was not improved in mice injected with LSTRA lymphoma or B16 melanoma.

  9. Anaerobic survival of Pseudomonas aeruginosa by pyruvate fermentation requires an Usp-type stress protein

    DEFF Research Database (Denmark)

    Schreiber, K; Boes, N; Escbach, M

    2006-01-01

    activity was detected in the deeper layers of a P. aeruginosa biofilm using a PPA3309-gfp (green fluorescent protein gene) fusion and confocal laser-scanning microscopy. This is the first description of an Anr-dependent, anaerobically induced, and functional Usp-like protein in bacteria....... the induced synthesis of three enzymes involved in arginine fermentation, ArcA, ArcB, and ArcC, and the outer membrane protein OprL. Moreover, formation of two proteins of unknown function, PA3309 and PA4352, increased by factors of 72- and 22-fold, respectively. Both belong to the group of universal stress...... proteins (Usp). Long-term survival of a PA3309 knockout mutant by pyruvate fermentation was found drastically reduced. The oxygen-sensing regulator Anr controls expression of the PPA3309-lacZ reporter gene fusion after a shift to anaerobic conditions and further pyruvate fermentation. PA3309 expression...

  10. Comparative changes in monthly blood urea nitrogen, total protein ...

    African Journals Online (AJOL)

    Sibanda M

    2015-03-29

    Mar 29, 2015 ... Comparative changes in monthly blood urea nitrogen, total protein concentrations, and body ... nitrogen (BUN) concentration, total protein (TP) concentration in blood serum and the body condition score ... BUN concentration, TP concentration and body condition scores of the animals were measured over.

  11. Comparative effect of local and foreign commercial feeds on the growth and survival of Clarias gariepinus juveniles

    Directory of Open Access Journals (Sweden)

    Moshood Keke Mustapha

    2014-07-01

    Full Text Available Growth and survival of Clarias gariepinus juveniles fed with a local feed and coppens commercial feed were observed for 16 weeks at the laboratory of the Department of Zoology, University of Ilorin, Nigeria. The proximate compositions and economics of the feeds and the water quality of the cultured tanks were assessed. Fish fed with coppens showed significant (P<0.05 higher weight increase, specific growth rate, protein efficiency ratio and low food conversion ratio than fish fed with local feed. Significant (P<0.05 higher mortality were recorded in fish fed with the local feed. The growth performance was a reflection of the proximate composition of the feeds with local feed having low crude protein (10.95%, lipid (3.95% and ash (4.92% when compared to coppens which had 42% crude protein, 12% lipid and 9.5% ash with protein being most significant. Carbohydrate (69.90% and crude fiber (2.88% were higher in the local feed than in coppens with an imbalance in carbohydrate and lipid ratio. Mortality was attributed to stress resulting from the poor quality of the feed. Cost of feeding with local feed to a weight gain of 31.67g was ₦80, while the cost of feeding with coppens to a weight gain of 148.58g was ₦16.

  12. Interaction of Erp Protein of Mycobacterium tuberculosis with Rv2212 Enhances Intracellular Survival of Mycobacterium smegmatis.

    Science.gov (United States)

    Ganaie, Arsheed Ahmad; Trivedi, Garima; Kaur, Amanpreet; Jha, Sidharth Shankar; Anand, Shashi; Rana, Vibhuti; Singh, Amit; Kumar, Shekhar; Sharma, Charu

    2016-10-15

    The Mycobacterium tuberculosis exported repetitive protein (RvErp) is a crucial virulence-associated factor as determined by its role in the survival and multiplication of mycobacteria in cultured macrophages and in vivo Although attempts have been made to understand the function of Erp protein, its exact role in Mycobacterium pathogenesis is still elusive. One way to determine this is by searching for novel interactions of RvErp. Using a yeast two-hybrid assay, an adenylyl cyclase (AC), Rv2212, was found to interact with RvErp. The interaction between RvErp and Rv2212 is direct and occurs at the endogenous level. The Erp protein of Mycobacterium smegmatis (MSMEG_6405, or MsErp) interacts neither with Rv2212 nor with Ms_4279, the M. smegmatis homologue of Rv2212. Deletion mutants of Rv2212 revealed its adenylyl cyclase domain to be responsible for the interaction. RvErp enhances Rv2212-mediated cyclic AMP (cAMP) production. Also, the biological significance of the interaction between RvErp and Rv2212 was demonstrated by the enhanced survival of M. smegmatis within THP-1 macrophages. Taken together, these studies address a novel mechanism by which Erp executes its function. RvErp is one of the important virulence factors of M. tuberculosis This study describes a novel function of RvErp protein of M. tuberculosis by identifying Rv2212 as its interacting protein. Rv2212 is an adenylyl cyclase (AC) and produces cAMP, one of the prime second messengers that regulate the intracellular survival of mycobacteria. Therefore, the significance of investigating novel interactions of RvErp is paramount in unraveling the mechanisms governing the intracellular survival of mycobacteria. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  13. Protein kinase G confers survival advantage to Mycobacterium tuberculosis during latency-like conditions.

    Science.gov (United States)

    Khan, Mehak Zahoor; Bhaskar, Ashima; Upadhyay, Sandeep; Kumari, Pooja; Rajmani, Raju S; Jain, Preeti; Singh, Amit; Kumar, Dhiraj; Bhavesh, Neel Sarovar; Nandicoori, Vinay Kumar

    2017-09-29

    Protein kinase G (PknG), a thioredoxin-fold-containing eukaryotic-like serine/threonine protein kinase, is a virulence factor in Mycobacterium tuberculosis, required for inhibition of phagolysosomal fusion. Here, we unraveled novel functional facets of PknG during latency-like conditions. We found that PknG mediates persistence under stressful conditions like hypoxia and abets drug tolerance. PknG mutant displayed minimal growth in nutrient-limited conditions, suggesting its role in modulating cellular metabolism. Intracellular metabolic profiling revealed that PknG is necessary for efficient metabolic adaptation during hypoxia. Notably, the PknG mutant exhibited a reductive shift in mycothiol redox potential and compromised stress response. Exposure to antibiotics and hypoxic environment resulted in higher oxidative shift in mycothiol redox potential of PknG mutant compared with the wild type. Persistence during latency-like conditions required kinase activity and thioredoxin motifs of PknG and is mediated through phosphorylation of a central metabolic regulator GarA. Finally, using a guinea pig model of infection, we assessed the in vivo role of PknG in manifestation of disease pathology and established a role for PknG in the formation of stable granuloma, hallmark structures of latent tuberculosis. Taken together, PknG-mediated GarA phosphorylation is important for maintenance of both mycobacterial physiology and redox poise, an axis that is dispensable for survival under normoxic conditions but is critical for non-replicating persistence of mycobacteria. In conclusion, we propose that PknG probably acts as a modulator of latency-associated signals. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Disease-free survival after complete mesocolic excision compared with conventional colon cancer surgery

    DEFF Research Database (Denmark)

    Bertelsen, Claus Anders; Neuenschwander, Anders Ulrich; Jansen, Jens Erik

    2015-01-01

    BACKGROUND: Application of the principles of total mesorectal excision to colon cancer by undertaking complete mesocolic excision (CME) has been proposed to improve oncological outcomes. We aimed to investigate whether implementation of CME improved disease-free survival compared with conventional...... consisted of patients who underwent CME surgery in a centre validated to perform such surgery; the control group consisted of patients undergoing conventional colon resection in three other hospitals. Data were collected from the Danish Colorectal Cancer Group (DCCG) database and medical charts. Patients...... updated by the National Central Office of Civil Registration. FINDINGS: The CME group consisted of 364 patients and the non-CME group consisted of 1031 patients. For all patients, 4-year disease-free survival was 85.8% (95% CI 81.4-90.1) after CME and 75.9% (72.2-79.7) after non-CME surgery (log-rank p=0...

  15. Anti-Inflammatory Heat Shock Protein 70 Genes are Positively Associated with Human Survival

    DEFF Research Database (Denmark)

    Singh, Ripudaman; Kølvraa, Steen; Bross, Peter Gerd

    2010-01-01

    with longevity. The involvement of heat shock protein 70 (Hsp70) in cellular maintenance and repair mechanisms, including its role as an anti-inflammatory protein, makes it a suitable candidate for studying such associations. We have studied the association of three single nucleotide polymorphisms, HSPA1A (-110A...... the opportunity to perform survival analysis on these subjects. Haplotype relative risk, and genotype relative risk were calculated to measure the effects of haplotypes and genotypes on human survival in a sex-specific manner. A significant association of HSPA1A-AA (RR=3.864; p=0.016) and HSPA1B-AA (RR=2.764; p=0...... observations from heat shock response (HSR) study where we had shown that after heat stimulation, mononuclear cells from the carriers of genotype HSPA1L-TT had better HSR than cells with the HSPA1L-CC genotype....

  16. Streptococcus gordonii collagen-binding domain protein CbdA may enhance bacterial survival in instrumented root canals ex vivo.

    Science.gov (United States)

    Moses, Peter J; Power, Daniel A; Jesionowski, Amy M; Jenkinson, Howard F; Pantera, Eugene A; Vickerman, M Margaret

    2013-01-01

    The surface-associated collagen-binding protein Ace of Enterococcus faecalis has been implicated as a virulence factor that contributes to bacterial persistence in endodontic infections. The purpose of this study was to determine if proteins with amino acid sequence similarity to Ace found in more abundant oral streptococci could play a similar role in potentially enhancing endodontic infections. A Streptococcus gordonii gene similar to ace was identified by genome sequence searches in silico. An isogenic derivative of strain DL1 with a disruption in the identified gene was constructed by allelic replacement. Parent and mutant strains were characterized for their ability to bind immobilized collagen type 1 in a microtiter plate-binding assay. Survival of the strains in a human tooth ex vivo-instrumented root canal model was compared by inoculating canals with parental or mutant bacteria and determining the colony-forming units (CFUs) recovered at various time points over a 12-day period. The S. gordonii gene, encoding a protein with a conserved collagen-binding domain similar to that of Ace, was designated cbdA. The cbdA-deficient cells were less able to bind collagen type 1 than parental cells (P < .0001). Genetic complementation of the cbdA-deficient strain restored the collagen-binding phenotype. By day 12, significantly fewer (P = .03) cbdA-deficient than parental CFUs were recovered from instrumented canals. A gene encoding a putative collagen-binding protein was identified in S. gordonii. Fewer S. gordonii cbdA-deficient cells survived ex vivo compared with parental cells, suggesting that collagen-binding proteins may contribute to the persistence of oral streptococci in instrumented root canals. Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  17. Comparative transcriptome analysis quantifies immune cell transcript levels, metastatic progression and survival in osteosarcoma.

    Science.gov (United States)

    Scott, Milcah C; Temiz, Nuri A; Sarver, Anne E; LaRue, Rebecca S; Rathe, Susan K; Varshney, Jyotika; Wolf, Natalie K; Moriarity, Branden S; O'Brien, Timothy D; Spector, Logan G; Largaespada, David A; Modiano, Jaime F; Subramanian, Subbaya; Sarver, Aaron L

    2017-10-24

    Overall survival of patients with osteosarcoma (OS) has improved little in the past three decades and better models for study are needed. OS is common in large dog breeds and is genetically inducible in mice, making the disease ideal for comparative genomic analyses across species. Understanding the level of conservation of inter-tumor transcriptional variation across species and how it is associated with progression to metastasis will enable us to more efficiently develop effective strategies to manage OS and improve therapy. In this study, transcriptional profiles of OS tumors and cell lines derived from humans (n=49), mice (n=103) and dogs (n=34) were generated using RNA-sequencing. Conserved inter-tumor transcriptional variation was present in tumor sets from all three species and comprised gene clusters associated with cell cycle and mitosis and with the presence or absence of immune cells. Further, we developed a novel Gene Cluster Expression Summary Score (GCESS) to quantify inter-tumor transcriptional variation and demonstrated that these GCESS values associated with patient outcome. Human OS tumors with GCESS values suggesting decreased immune cell presence were associated with metastasis and poor survival. We validated these results in an independent human OS tumor cohort and in 15 different tumor data sets obtained from The Cancer Genome Atlas (TCGA). Our results suggest that quantification of immune cell absence and tumor cell proliferation may better inform therapeutic decisions and improve overall survival for OS patients. Copyright ©2017, American Association for Cancer Research.

  18. Effects of sugar alcohol and proteins on the survival of Lactobacillus bulgaricus LB6 during freeze drying.

    Science.gov (United States)

    Chen, He; Chen, Shiwei; Chen, Hongli; Wu, Yanyan; Shu, Guowei

    2015-01-01

    Lactobacillus bulgaricus LB6 is a bacterium which was selected in the commercial yoghurt with high angiotensin converting enzyme (ACE) inhibitory activity. Preparation of concentrated starter cultures via freeze drying is of practical importance to dairy and food industries. We optimized the optimal sugar alcohol and proteins for Lactobacillus bulgaricus LB6 during the process of freeze drying using a Plackett-Burman design. In our initial tests survival rate and the number of viable cells were associated with the type of lyoprotectant used and so our optimization protocol focused on increasing survival rate. Substances that had previously had a protective effect during freeze drying were investigated, for example: mannitol, sorbitol, xylitol, meso-erythritol, lactitol, whey protein isolate 90, bovine serum albumin, and whey protein concentrate 80 and soy protein isolate 70. We found that the optimum sugar alcohol and proteins for survival of Lactobacillus bulgaricus LB6 were whey protein concentrate (p = 0.0040 for survival rate), xylitol (p = 0.0067 for survival rate) and sorbitol (p = 0.0073 for survival rate), they showed positive effect (whey protein concentrate and sorbitol) or negative effect (xylitol). The effectiveness of three chosen sugar alcohols and protein implied that they could be used as lyoprotectant for Lactobacillus bulgaricus LB6 in the further research, the optimal composition of sugar alcohol and protein for the lyoprotectant use must be established.

  19. High ERK Protein Expression Levels Correlate with Shorter Survival in Triple-Negative Breast Cancer Patients

    Science.gov (United States)

    Gonzalez-Angulo, Ana M.; Liu, Ping; Hayashi, Naoki; Lluch, Ana; Ferrer-Lozano, Jaime; Hortobágyi, Gabriel N.

    2012-01-01

    The mitogen-activated protein kinase (MAPK) signaling pathway is known to be activated in triple-negative breast cancer (TNBC). Extracellular signal–related kinase (ERK), a member of the MAPK pathway, promotes cell proliferation, angiogenesis, cell differentiation, and cell survival. To assess the prognostic impact of ERK in TNBC patients, relative quantities of ERK (ERK-2 and pMAPK) and direct targets of the ERK pathway (MAPK/ERK kinase 1, phospho-enriched protein in astrocytes [PEA]-15, phosphorylated (p)PEA-15, tuberous sclerosis protein 2, p70S6 kinase, and p27) were measured using reverse-phase protein arrays in tumor tissue from patients with TNBC (n = 97) and non-TNBC (n = 223). Protein levels in patients with TNBC were correlated with clinical and tumor characteristics and outcome. The median age of patients with TNBC was 55 years (range, 27–86 years). Disease stage was I in 21%, II in 60%, and III in 20% of the patients. In a multivariate analysis, among patients with TNBC, those with ERK-2–overexpressing tumors had a lower overall survival rate than those with low ERK-2–expressing tumors (hazard ratio [HR], 2.76; 95% confidence interval [CI], 1.19–6.41). However, high pMAPK levels were associated with a significantly higher relapse-free survival rate (HR, 0.66; 95% CI, 0.46–0.95). In conclusion, ERK-2 and pMAPK are valuable prognostic markers in TNBC. Further studies are justified to elucidate ERK's role in TNBC tumorigenicity and metastasis. PMID:22584435

  20. ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

    OpenAIRE

    Capra, John A.; Williams, Alexander G.; Pollard, Katherine S.

    2012-01-01

    The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight into the cellular functions and interactions of proteins, such comparative phylogenetic analyses are rarely performed, because they require custom algorithms. We developed ProteinHistorian to make too...

  1. Protein C concentrate controls leukocyte recruitment during inflammation and improves survival during endotoxemia after efficient in vivo activation.

    Science.gov (United States)

    Frommhold, David; Tschada, Julia; Braach, Natascha; Buschmann, Kirsten; Doerner, Axel; Pflaum, Johanna; Stahl, Marie-Sophie; Wang, Hongjie; Koch, Lutz; Sperandio, Markus; Bierhaus, Angelika; Isermann, Berend; Poeschl, Johannes

    2011-11-01

    Anti-inflammatory properties of protein C (PC) concentrate are poorly studied compared to activated protein C, although PC is suggested to be safer in clinical use. We investigated how PC interferes with the leukocyte recruitment cascade during acute inflammation and its efficacy during murine endotoxemia. We found that similar to activated protein infusion, intravenous PC application reduced leukocyte recruitment in inflamed tissues in a dose- and time-dependent manner. During both tumor necrosis factor-α induced and trauma-induced inflammation of the cremaster muscle, intravital microscopy revealed that leukocyte adhesion and transmigration, but not rolling, were profoundly inhibited by 100 U/kg PC. Moreover, PC blocked leukocyte emigration into the bronchoalveolar space during lipopolysaccharide (LPS) induced acute lung injury. PC was efficiently activated in a murine endotoxemia model, which reduced leukocyte infiltration of organs and strongly improved survival (75% versus 25% of control mice). Dependent on the inflammatory model, PC provoked a significant inhibition of leukocyte recruitment as early as 1 hour after administration. PC-induced inhibition of leukocyte recruitment during acute inflammation critically involves thrombomodulin-mediated PC activation, subsequent endothelial PC receptor and protease-activated receptor-1-dependent signaling, and down-regulation of intercellular adhesion molecule 1 leading to reduced endothelial inflammatory response. We conclude that during acute inflammation and sepsis, PC is a fast acting and effective therapeutic approach to block leukocyte recruitment and improve survival. Copyright © 2011 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  2. Survival of Listeria innocua in rainbow trout protein recovered by isoelectric solubilization and precipitation with acetic and citric acids.

    Science.gov (United States)

    Otto, R A; Paker, I; Bane, L; Beamer, S; Jaczynski, J; Matak, K E

    2011-08-01

    During mechanical fish processing, a substantial amount of protein is discarded as by-products. Isoelectric solubilization and precipitation (ISP) is a process that uses extreme pH shifts to solubilize and precipitate protein from by-products to recover previously discarded protein. Typically, strong acids are used for pH reduction, but these acids do not have a pasteurization effect (6 log reduction) on bacterial load; therefore, organic acids were used during ISP processing to test the impact on Listeria innocua concentrations. Headed and gutted rainbow trout (Oncorhynchus mykiss) were inoculated with L. innocua, homogenized, and brought to the target pH with granular citric acid (pH 2.0 and 2.5) or glacial acetic acid (pH 3.0 and 3.5). Proteins were solubilized for 10 min at 4°C, and insoluble components (e.g., skin and insoluble protein) were removed by centrifugation. The remaining solution was pH shifted to the protein isoelectric point (pH 5.5) with sodium hydroxide, and precipitated protein was separated from the water. Microbial cells for each component (proteins, insolubles, and water) were enumerated on modified Oxford agar (MOX) and tryptic soy agar with 6% yeast extract (TSAYE). The sums of the surviving cells from each component were compared with the initial inoculum levels. No significant differences were observed between results obtained from TSAYE and from MOX (P > 0.05). Significant reductions in microbial populations were detected, regardless of pH or acid type (P acid, resulting in a mean reduction of 6.41 log CFU/g in the recovered protein and 5.88 log CFU/g in the combined components. These results demonstrate the antimicrobial potential of organic acids in ISP processing.

  3. Nivolumab versus Cabozantinib: Comparing Overall Survival in Metastatic Renal Cell Carcinoma.

    Directory of Open Access Journals (Sweden)

    Witold Wiecek

    Full Text Available Renal-cell carcinoma (RCC affects over 330,000 new patients every year, of whom 1/3 present with metastatic RCC (mRCC at diagnosis. Most mRCC patients treated with a first-line agent relapse within 1 year and need second-line therapy. The present study aims to compare overall survival (OS between nivolumab and cabozantinib from two recent pivotal studies comparing, respectively, each one of the two emerging treatments against everolimus in patients who relapse following first-line treatment. Comparison is traditionally carried out using the Bucher method, which assumes proportional hazard. Since OS curves intersected in one of the pivotal studies, models not assuming proportional hazards were also considered to refine the comparison. Four Bayesian parametric survival network meta-analysis models were implemented on overall survival (OS data digitized from the Kaplan-Meier curves reported in the studies. Three models allowing hazard ratios (HR to vary over time were assessed against a fixed-HR model. The Bucher method favored cabozantinib, with a fixed HR for OS vs. nivolumab of 1.09 (95% confidence interval: [0.77, 1.54]. However, all models with time-varying HR showed better fits than the fixed-HR model. The log-logistic model fitted the data best, exhibiting a HR for OS initially favoring cabozantinib, the trend inverting to favor nivolumab after month 5 (95% credible interval <1 from 10 months. The initial probability of cabozantinib conferring superior OS was 54%, falling to 41.5% by month 24. Numerical differences in study-adjusted OS estimates between the two treatments remained small. This study evidences that HR for OS of nivolumab vs. cabozantinib varies over time, favoring cabozantinib in the first months of treatment but nivolumab afterwards, a possible indication that patients with poor prognosis benefit more from cabozantinib in terms of survival, nivolumab benefiting patients with better prognosis. More evidence, including real

  4. Comparative proteome analysis of egg yolk plasma proteins during storage.

    Science.gov (United States)

    Gao, Dan; Qiu, Ning; Liu, Yaping; Ma, Meihu

    2017-06-01

    Physical changes such as chicken egg white thinning and egg yolk flattening occur during storage, implying a decline in egg quality. To reveal the deteriorative process related to chicken egg internal quality, a comparative proteomic method was used in this study to analyze the alterations in egg yolk plasma proteins at different storage times (0, 20 and 40 days) under an ambient temperature of 22 ± 2 °C. Using two-dimensional electrophoresis followed by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry, 33 protein spots representing 12 proteins were identified with significant (P albumin, vitellogenin fragments, IgY chains, ovalbumin, ovoinhibitor, α 2 -macroglobulin-like protein 1-like, hemopexin, transthyretin, apolipoprotein A-I and β 2 -glycoprotein I precursor. Accelerating degradation for most egg yolk plasma proteins was observed after prolonged storage (from day 20 to day 40). It is likely that the increased degradation of protease inhibitors such as ovoinhibitor and α 2 -macroglobulin-like protein 1-like during prolonged storage lead to an imbalance of protease and antiprotease in egg yolk, which may play a key role in the degradation of egg yolk proteins. These findings will provide an insight into the effects of storage on egg yolk protein changes and give a deeper understanding of the deteriorative process of chicken egg yolk. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  5. Associations between lamb survival and prion protein genotype: analysis of data for ten sheep breeds in Great Britain

    Directory of Open Access Journals (Sweden)

    Bishop Stephen C

    2009-01-01

    Full Text Available Abstract Background Selective breeding programmes, based on prion protein (PrP genotype, have been introduced throughout the European Union to reduce the risk of sheep transmissible spongiform encephalopathies (TSEs. These programmes could have negative consequences on other important traits, such as fitness and production traits, if the PrP gene has pleiotropic effects or is in linkage disequilibrium with genes affecting these traits. This paper presents the results of an investigation into associations between lamb survival and PrP genotype in ten mainstream sheep breeds in Great Britain (GB. In addition, the reasons for lamb deaths were examined in order to identify any associations between these and PrP genotype. Results Survival times from birth to weaning were analysed for over 38000 lambs (2427 dead and 36096 live lambs from 128 flocks using Cox proportional hazard models for each breed, including additive animal genetic effects. No significant associations between PrP genotype and lamb survival were identified, except in the Charollais breed for which there was a higher risk of mortality in lambs of the ARR/VRQ genotype compared with those of the ARR/ARR genotype. Significant effects of birth weight, litter size, sex, age of dam and year of birth on survival were also identified. For all breeds the reasons for death changed significantly with age; however, no significant associations between reason for death and PrP genotype were found for any of the breeds. Conclusion This study found no evidence to suggest that a selective breeding programme based on PrP genotype will have a detrimental effect on lamb survival. The only significant effect of PrP genotype identified was likely to be of little consequence because an increased risk of mortality was associated with a genotype that is selected against in current breeding strategies.

  6. Using an alignment of fragment strings for comparing protein structures

    DEFF Research Database (Denmark)

    Friedberg, Iddo; Harder, Tim; Kolodny, Rachel

    2007-01-01

    MOTIVATION: Most methods that are used to compare protein structures use three-dimensional (3D) structural information. At the same time, it has been shown that a 1D string representation of local protein structure retains a degree of structural information. This type of representation can be a p....... The results of this study have immediate applications towards fast structure recognition, and for fold prediction and classification.......MOTIVATION: Most methods that are used to compare protein structures use three-dimensional (3D) structural information. At the same time, it has been shown that a 1D string representation of local protein structure retains a degree of structural information. This type of representation can...... be a powerful tool for protein structure comparison and classification, given the arsenal of sequence comparison tools developed by computational biology. However, in order to do so, there is a need to first understand how much information is contained in various possible 1D representations of protein structure...

  7. Comparative Study of Elastic Network Model and Protein Contact Network for Protein Complexes: The Hemoglobin Case

    Directory of Open Access Journals (Sweden)

    Guang Hu

    2017-01-01

    Full Text Available The overall topology and interfacial interactions play key roles in understanding structural and functional principles of protein complexes. Elastic Network Model (ENM and Protein Contact Network (PCN are two widely used methods for high throughput investigation of structures and interactions within protein complexes. In this work, the comparative analysis of ENM and PCN relative to hemoglobin (Hb was taken as case study. We examine four types of structural and dynamical paradigms, namely, conformational change between different states of Hbs, modular analysis, allosteric mechanisms studies, and interface characterization of an Hb. The comparative study shows that ENM has an advantage in studying dynamical properties and protein-protein interfaces, while PCN is better for describing protein structures quantitatively both from local and from global levels. We suggest that the integration of ENM and PCN would give a potential but powerful tool in structural systems biology.

  8. Comparative changes in monthly blood urea nitrogen, total protein ...

    African Journals Online (AJOL)

    The objective of this study was to determine the comparative changes in the monthly blood urea nitrogen (BUN) concentration, total protein (TP) concentration in blood serum and the body condition score of Nguni cows and heifers raised on sweetveld. Twenty-four clinically healthy animals in different parities, namely Parity ...

  9. Survival of diabetes patients with major amputation is comparable to malignant disease.

    Science.gov (United States)

    Hoffmann, Martin; Kujath, Peter; Flemming, Annette; Proß, Moritz; Begum, Nehara; Zimmermann, Markus; Keck, Tobias; Kleemann, Markus; Schloericke, Erik

    2015-07-01

    Almost all studies on diabetic foot syndrome focused on prevention of amputation and did not investigate long-term prognosis and survival of patients as a primary outcome parameter. We did a retrospective cohort study including 314 patients who had diabetic foot syndrome and underwent amputation between December 1995 and January 2001. A total of 48% of patients received minor amputation (group I), 15% only major amputation (group II) and 36% initially underwent a minor amputation that was followed by a major amputation (group III). Statistically significant differences were observed in comparison of the median survival of group I to group II (51 vs. 40 months; p = 0.016) and of group II to group III (40 vs. 55 months; p = 0.003). The prognosis of patients with major amputation due to diabetic foot syndrome is comparable to patients with malignant diseases. Vascular interventions did not improve the individual prognosis of patients. © The Author(s) 2015.

  10. Comparative Effectiveness of Cancer Control and Survival after Robot-Assisted versus Open Radical Prostatectomy.

    Science.gov (United States)

    Hu, Jim C; O'Malley, Padraic; Chughtai, Bilal; Isaacs, Abby; Mao, Jialin; Wright, Jason D; Hershman, Dawn; Sedrakyan, Art

    2017-01-01

    Robot-assisted surgery has been rapidly adopted in the U.S. for prostate cancer. Its adoption has been driven by market forces and patient preference, and debate continues regarding whether it offers improved outcomes to justify the higher cost relative to open surgery. We examined the comparative effectiveness of robot-assisted vs open radical prostatectomy in cancer control and survival in a nationally representative population. This population based observational cohort study of patients with prostate cancer undergoing robot-assisted radical prostatectomy and open radical prostatectomy during 2003 to 2012 used data captured in the SEER (Surveillance, Epidemiology, and End Results)-Medicare linked database. Propensity score matching and time to event analysis were used to compare all cause mortality, prostate cancer specific mortality and use of additional treatment after surgery. A total of 6,430 robot-assisted radical prostatectomies and 9,161 open radical prostatectomies performed during 2003 to 2012 were identified. The use of robot-assisted radical prostatectomy increased from 13.6% in 2003 to 2004 to 72.6% in 2011 to 2012. After a median followup of 6.5 years (IQR 5.2-7.9) robot-assisted radical prostatectomy was associated with an equivalent risk of all cause mortality (HR 0.85, 0.72-1.01) and similar cancer specific mortality (HR 0.85, 0.50-1.43) vs open radical prostatectomy. Robot-assisted radical prostatectomy was also associated with less use of additional treatment (HR 0.78, 0.70-0.86). Robot-assisted radical prostatectomy has comparable intermediate cancer control as evidenced by less use of additional postoperative cancer therapies and equivalent cancer specific and overall survival. Longer term followup is needed to assess for differences in prostate cancer specific survival, which was similar during intermediate followup. Our findings have significant quality and cost implications, and provide reassurance regarding the adoption of more

  11. N-terminal protein processing: A comparative proteogenomic analysis

    Energy Technology Data Exchange (ETDEWEB)

    Bonissone, Stefano; Gupta, Nitin; Romine, Margaret F.; Bradshaw, Ralph A.; Pevzner, Pavel A.

    2013-01-01

    N-Terminal Methionine Excision (NME) is a universally conserved mechanism with the same specificity across all life forms that removes the first Methionine in proteins when the second residue is Gly, Ala, Ser, Cys, Thr, Pro, or Val. In spite of its necessity for proper cell functioning, the functional role of NME remains unclear. In 1988, Arfin and Bradshaw connected NME with the N-end protein degradation rule and postulated that the role of NME is to expose the stabilizing residues with the goal to resist protein degradation. While this explanation (that treats 7 stabilizing residues in the same manner) has become the de facto dogma of NME, comparative proteogenomics analysis of NME tells a different story. We suggest that the primary role of NME is to expose only two (rather than seven) amino acids Ala and Ser for post-translational modifications (e.g., acetylation) rather than to regulate protein degradation. We argue that, contrary to the existing view, NME is not crucially important for proteins with 5 other stabilizing residue at the 2nd positions that are merely bystanders (their function is not affected by NME) that become exposed to NME because their sizes are comparable or smaller than the size of Ala and Ser.

  12. Vaccination with Recombinant Non-transmembrane Domain of Protein Mannosyltransferase 4 Improves Survival during Murine Disseminated Candidiasis.

    Science.gov (United States)

    Wang, Li; Yan, Lan; Li, Xing Xing; Xu, Guo Tong; An, Mao Mao; Jiang, Yuan Ying

    2015-01-01

    Candida albicans is the most common cause of invasive fungal infections in humans. The C. albicans cell wall proteins play an important role in crucial host-fungus interactions and might be ideal vaccine targets to induce protective immune response in host. Meanwhile, protein that is specific to C. albicans is also an ideal target of vaccine. In this study, 11 proteins involving cell wall biosynthesis, yeast-to-hypha formation, or specific to C. albicans were chosen and were successfully cloned, purified and verified. The immune protection of vaccination with each recombinant protein respectively in preventing systemic candidiasis in BALB/c mice was assessed. The injection of rPmt4p vaccination significantly increased survival rate, decreased fungal burdens in the heart, liver, brain, and kidneys, and increased serum levels of both immunoglobulin G (IgG) and IgM against rPmt4p in the immunized mice. Histopathological assessment demonstrated that rPmt4p vaccination protected the tissue structure, and decreased the infiltration of inflammatory cells. Passive transfer of the rPmt4p immunized serum increased survival rate against murine systemic candidiasis and significantly reduced organ fungal burden. The immune serum enhanced mouse neutrophil killing activity by directly neutralizing rPmt4p effects in vitro. Levels of interleukin (IL)-4, IL-10, IL-12p70, IL-17A and tumor necrosis factor (TNF)-α in serum were higher in the immunized mice compared to those in the adjuvant control group. In conclusion, our results suggested that rPmt4p vaccination may be considered as a potential vaccine candidate against systemic candidiasis.

  13. Adjusting for treatment switching in the METRIC study shows further improved overall survival with trametinib compared with chemotherapy.

    Science.gov (United States)

    Latimer, Nicholas R; Bell, Helen; Abrams, Keith R; Amonkar, Mayur M; Casey, Michelle

    2016-05-01

    Trametinib, a selective inhibitor of mitogen-activated protein kinase kinase 1 (MEK1) and MEK2, significantly improves progression-free survival compared with chemotherapy in patients with BRAF V600E/K mutation-positive advanced or metastatic melanoma (MM). However, the pivotal clinical trial permitted randomized chemotherapy control group patients to switch to trametinib after disease progression, which confounded estimates of the overall survival (OS) advantage of trametinib. Our purpose was to estimate the switching-adjusted treatment effect of trametinib for OS and assess the suitability of each adjustment method in the primary efficacy population. Of the patients randomized to chemotherapy, 67.4% switched to trametinib. We applied the rank-preserving structural failure time model, inverse probability of censoring weights, and a two-stage accelerated failure time model to obtain estimates of the relative treatment effect adjusted for switching. The intent-to-treat (ITT) analysis estimated a 28% reduction in the hazard of death with trametinib treatment (hazard ratio [HR], 0.72; 95% CI, 0.52-0.98) for patients in the primary efficacy population (data cut May 20, 2013). Adjustment analyses deemed plausible provided OS HR point estimates ranging from 0.48 to 0.53. Similar reductions in the HR were estimated for the first-line metastatic subgroup. Treatment with trametinib, compared with chemotherapy, significantly reduced the risk of death and risk of disease progression in patients with BRAF V600E/K mutation-positive advanced melanoma or MM. Adjusting for switching resulted in lower HRs than those obtained from standard ITT analyses. However, CI are wide and results are sensitive to the assumptions associated with each adjustment method. © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

  14. Better survival of hybrid total knee arthroplasty compared to cemented arthroplasty

    Science.gov (United States)

    Petursson, Gunnar; Fenstad, Anne Marie; Havelin, Leif Ivar; Gøthesen, Øystein; Lygre, Stein Håkon Låstad; Röhrl, Stephan M; Furnes, Ove

    2015-01-01

    Background and purpose — There have been few comparative studies on total knee replacement (TKR) with cemented tibia and uncemented femur (hybrid TKR). Previous studies have not shown any difference in revision rate between cemented and hybrid fixation, but these studies had few hybrid prostheses. We have evaluated the outcome of hybrid TKR based on data from the Norwegian Arthroplasty Register (NAR). Patients and methods — We compared 4,585 hybrid TKRs to 20,095 cemented TKRs with risk of revision for any cause as the primary endpoint. We included primary TKRs without patella resurfacing that were reported to the NAR during the years 1999–2012. To minimize the possible confounding effect of prosthesis brands, only brands that were used both as hybrids and cemented in more than 200 cases were included. Kaplan-Meier survival analysis and Cox regression analysis were done with adjustment for age, sex, and preoperative diagnosis. To include death as a competing risk, cumulative incidence function estimates were calculated. Results — Estimated survival at 11 years was 94.3% (95% CI: 93.9–94.7) in the cemented TKR group and 96.3% (CI: 95.3–97.3) in the hybrid TKR group. The adjusted Cox regression analysis showed a lower risk of revision in the hybrid group (relative risk = 0.58, CI: 0.48–0.72, p hybrid group included 3 brands of prostheses: LCS classic, LCS complete, and Profix. Profix hybrid TKR had lower risk of revision than cemented TKR, but the LCS classic and LCS complete did not. Kaplan-Meier estimated survival at 11 years was 96.8% (CI: 95.6–98.0) in the hybrid Profix group and 95.2% (CI: 94.6–95.8) in the cemented Profix group. Mean operating time was 17 min longer in the cemented group. Interpretation — Survivorship of the hybrid TKR at 11 years was better than that for cemented TKR, or the same, depending on the brand of prosthesis. Hybrid fixation appears to be a safe and time-efficient alternative to cemented fixation in total knee

  15. Expression of the SNARE protein SNAP-23 is essential for cell survival.

    Science.gov (United States)

    Kaul, Sunil; Mittal, Sharad K; Feigenbaum, Lionel; Kruhlak, Michael J; Roche, Paul A

    2015-01-01

    Members of the SNARE-family of proteins are known to be key regulators of the membrane-membrane fusion events required for intracellular membrane traffic. The ubiquitously expressed SNARE protein SNAP-23 regulates a wide variety of exocytosis events and is essential for mouse development. Germline deletion of SNAP-23 results in early embryonic lethality in mice, and for this reason we now describe mice and cell lines in which SNAP-23 can be conditionally-deleted using Cre-lox technology. Deletion of SNAP-23 in CD19-Cre expressing mice prevents B lymphocyte development and deletion of SNAP-23 using a variety of T lymphocyte-specific Cre mice prevents T lymphocyte development. Acute depletion of SNAP-23 in mouse fibroblasts leads to rapid apoptotic cell death. These data highlight the importance of SNAP-23 for cell survival and describe a mouse in which specific cell types can be eliminated by expression of tissue-specific Cre-recombinase.

  16. Chaperones and multitasking proteins in the nucleolus: networking together for survival?

    Science.gov (United States)

    Bański, Piotr; Kodiha, Mohamed; Stochaj, Ursula

    2010-07-01

    The nucleolus has emerged as a key player that regulates cell growth, survival and the recovery from stress. Progress in proteomics made it possible to sequence the nucleolar proteome under different physiological conditions. Together with other research, this work revealed the presence of multiple chaperones and co-chaperones in the nucleolus. Molecular chaperones are components of a larger network that promotes protein homeostasis, thereby providing continuous adaptation to a changing environment. Recent studies suggest that the cellular chaperone network is divided into individual branches which orchestrate specific functions. Input from separate branches is then combined to 'fine-tune' the cellular proteostasis network. Based on the latest developments in nucleolar and chaperone biology, we speculate that a unique network comprising chaperones, co-chaperones and multitasking proteins is located in nucleoli. This network supports and regulates fundamental biological processes, including ribosome biogenesis, cell signaling, and the stress response. Copyright 2010 Elsevier Ltd. All rights reserved.

  17. Effect of a long-term high-protein diet on survival, obesity development, and gut microbiota in mice.

    Science.gov (United States)

    Kiilerich, Pia; Myrmel, Lene Secher; Fjære, Even; Hao, Qin; Hugenholtz, Floor; Sonne, Si Brask; Derrien, Muriel; Pedersen, Lone Møller; Petersen, Rasmus Koefoed; Mortensen, Alicja; Licht, Tine Rask; Rømer, Maria Unni; Vogel, Ulla Birgitte; Waagbø, Linn Jeanette; Giallourou, Natasa; Feng, Qiang; Xiao, Liang; Liu, Chuan; Liaset, Bjørn; Kleerebezem, Michiel; Wang, Jun; Madsen, Lise; Kristiansen, Karsten

    2016-06-01

    Female C57BL/6J mice were fed a regular low-fat diet or high-fat diets combined with either high or low protein-to-sucrose ratios during their entire lifespan to examine the long-term effects on obesity development, gut microbiota, and survival. Intake of a high-fat diet with a low protein/sucrose ratio precipitated obesity and reduced survival relative to mice fed a low-fat diet. By contrast, intake of a high-fat diet with a high protein/sucrose ratio attenuated lifelong weight gain and adipose tissue expansion, and survival was not significantly altered relative to low-fat-fed mice. Our findings support the notion that reduced survival in response to high-fat/high-sucrose feeding is linked to obesity development. Digital gene expression analyses, further validated by qPCR, demonstrated that the protein/sucrose ratio modulated global gene expression over time in liver and adipose tissue, affecting pathways related to metabolism and inflammation. Analysis of fecal bacterial DNA using the Mouse Intestinal Tract Chip revealed significant changes in the composition of the gut microbiota in relation to host age and dietary fat content, but not the protein/sucrose ratio. Accordingly, dietary fat rather than the protein/sucrose ratio or adiposity is a major driver shaping the gut microbiota, whereas the effect of a high-fat diet on survival is dependent on the protein/sucrose ratio. Copyright © 2016 the American Physiological Society.

  18. Inhibition of Bcl-2 or IAP proteins does not provoke mutations in surviving cells

    Energy Technology Data Exchange (ETDEWEB)

    Shekhar, Tanmay M. [Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora 3083 (Australia); Green, Maja M. [Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora 3083 (Australia); Department of Anatomy & Neuroscience, The University of Melbourne, Parkville 3010 (Australia); Rayner, David M.; Miles, Mark A.; Cutts, Suzanne M. [Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora 3083 (Australia); Hawkins, Christine J., E-mail: c.hawkins@latrobe.edu.au [Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora 3083 (Australia)

    2015-07-15

    Graphical abstract: - Highlights: • Mutagenicities of anti-cancer drugs were tested using HPRT, γH2AX and comet assays. • TRAIL, doxorubicin and etoposide were more mutagenic than BH3- or Smac-mimetics. • Physiologically achievable levels of the BH3-mimetic ABT-737 were not mutagenic. • High concentrations of ABT-737 provoked mutations via an off-target mechanism. • Even very high concentrations of IAP antagonists were not mutagenic. - Abstract: Chemotherapy and radiotherapy can cause permanent damage to the genomes of surviving cells, provoking severe side effects such as second malignancies in some cancer survivors. Drugs that mimic the activity of death ligands, or antagonise pro-survival proteins of the Bcl-2 or IAP families have yielded encouraging results in animal experiments and early phase clinical trials. Because these agents directly engage apoptosis pathways, rather than damaging DNA to indirectly provoke tumour cell death, we reasoned that they may offer another important advantage over conventional therapies: minimisation or elimination of side effects such as second cancers that result from mutation of surviving normal cells. Disappointingly, however, we previously found that concentrations of death receptor agonists like TRAIL that would be present in vivo in clinical settings provoked DNA damage in surviving cells. In this study, we used cell line model systems to investigate the mutagenic capacity of drugs from two other classes of direct apoptosis-inducing agents: the BH3-mimetic ABT-737 and the IAP antagonists LCL161 and AT-406. Encouragingly, our data suggest that IAP antagonists possess negligible genotoxic activity. Doses of ABT-737 that were required to damage DNA stimulated Bax/Bak-independent signalling and exceeded concentrations detected in the plasma of animals treated with this drug. These findings provide hope that cancer patients treated by BH3-mimetics or IAP antagonists may avoid mutation-related illnesses that afflict

  19. Survival after liver transplantation in cirrhotic patients with and without hepatocellular carcinoma: a comparative study.

    Science.gov (United States)

    Figueras, J; Jaurrieta, E; Valls, C; Benasco, C; Rafecas, A; Xiol, X; Fabregat, J; Casanovas, T; Torras, J; Baliellas, C; Ibañez, L; Moreno, P; Casais, L

    1997-06-01

    Cumulative recurrence after surgical resection for hepatocellular carcinoma (HCC) is very high. Several retrospective analyses have shown that liver transplantation was more effective than resection for patients with HCC at early tumor stages. Consequently, in January 1990, we decided to prospectively indicate orthotopic liver transplantation (OLT) as the first surgical treatment for small, localized HCC in cirrhotic patients without nodal involvement independently of the degree of liver function. The aim of this prospective cohort study was to analyze prognosis, recurrence rate, and survival after liver transplantation in patients in whom the main indication was HCC with cirrhosis. Thirty-eight patients in whom the main indication for liver transplantation was HCC and hepatic cirrhosis were compared with 136 transplantations because of cirrhosis without tumor, performed in our unit from January 1990 to December 1995. HCC arising in noncirrhotic livers and those incidently discovered after OLT were excluded from the study. Chemoembolization using doxorubicin, lipiodol, and Gelfoam was performed before OLT in 31 patients with good liver function. There were no differences in gender, but HCC patients were older (57 +/- 7 vs. 50 +/- 10 years [P < .001]). Liver function was better in HCC (Child-Pugh score: 6.9 +/- 2 vs. 8.6 +/- 1.8; P < .001), and hepatitis C virus antibody was positive in 31 (82%) vs. 51 (37%) (P < .007). Seven tumors had bilobar involvement (18%). Capsule was present in 22 (58%). The mean size of the tumor was 3.4 +/- 2 cm. Seventeen tumors (45%) were larger than 3 cm, and 4 (11%) were larger than 5 cm. The average number of nodules was 2 +/- 1. The tumor-node-metastasis stage of the tumors was pT1 in 6 patients (16%), 11 were pT2 (29%), 12 were pT3 (31%), and 9 were pT4 (24%). Seven patients were retransplanted in the HCC group (18%) and 19 (14%) in the nontumor group (not significant). Tumor recurrence was detected in three patients (8%). One, 3

  20. Comparing measurement error correction methods for rate-of-change exposure variables in survival analysis.

    Science.gov (United States)

    Veronesi, Giovanni; Ferrario, Marco M; Chambless, Lloyd E

    2013-12-01

    In this article we focus on comparing measurement error correction methods for rate-of-change exposure variables in survival analysis, when longitudinal data are observed prior to the follow-up time. Motivational examples include the analysis of the association between changes in cardiovascular risk factors and subsequent onset of coronary events. We derive a measurement error model for the rate of change, estimated through subject-specific linear regression, assuming an additive measurement error model for the time-specific measurements. The rate of change is then included as a time-invariant variable in a Cox proportional hazards model, adjusting for the first time-specific measurement (baseline) and an error-free covariate. In a simulation study, we compared bias, standard deviation and mean squared error (MSE) for the regression calibration (RC) and the simulation-extrapolation (SIMEX) estimators. Our findings indicate that when the amount of measurement error is substantial, RC should be the preferred method, since it has smaller MSE for estimating the coefficients of the rate of change and of the variable measured without error. However, when the amount of measurement error is small, the choice of the method should take into account the event rate in the population and the effect size to be estimated. An application to an observational study, as well as examples of published studies where our model could have been applied, are also provided.

  1. Positive expression of p53, c-erbB2 and MRP proteins is correlated with survival rates of NSCLC patients.

    Science.gov (United States)

    Xu, Yujin; Wang, Liancong; Zheng, Xiao; Liu, Guan; Wang, Yuezhen; Lai, Xiaojing; Li, Jianqiang

    2013-05-01

    The incidence of lung cancer is one of the leading causes of mortality. This study aimed to investigate the prognostic and predictive importance of p53, c-erbB2 and multidrug resistance proteins (MRP) expression and its correlation with clinicopathological characteristics of patients with non-small cell lung cancer (NSCLC). Expression of p53, c-erbB2 and MRP proteins in 152 tumor samples from resected primary NSCLCs was detected by immunohistochemical staining. The correlation of proteins, survival and clinicopathological characteristics was investigated in 152 patients undergoing potentially curative surgery. The positive rates of p53, c-erbB2 and MRP expression were 53.9 (82/152), 44.1 (67/152) and 43.4% (66/152), respectively. Overall survival rates of patients were markedly correlated with the overexpression of p53, c-erbB2 and MRP proteins. One, 2- and 3-year survival rates of patients exhibiting a positive expression of these proteins were 72.6, 54.8 and 32.2%, respectively. These rates were lower compared with those of patients with a negative expression of these proteins (92.1, 78.5 and 63.4%) (P=0.02, 0.01 or 0.00, respectively). Results of Cox's regression analysis showed that c-erbB2 expression and cell differentiation were independent prognostic factors in patients with NSCLC. These findings suggest that the positive expression of p53, c-erbB2 and MRP proteins is correlated with the survival rates of NSCLC patients. Detection of positive p53, c-erbB2 and MRP expression may be a useful predictive indicator of prognosis. Positive c-erbB2 expression is an independent prognostic factor, with a potential to be used as a predictive indicator of chemotherapy efficacy in NSCLC patients.

  2. Survival and growth compared between wild and farmed eel stocked in freshwater ponds

    DEFF Research Database (Denmark)

    Pedersen, Michael Ingemann; Jepsen, Niels; Rasmussen, Gorm

    2017-01-01

    conducted in a series of shallow, open ponds of approximately 200 m2. Wild and farmed eels were batch tagged, mixed and released in the ponds at an initial density of 0.5 individual/m2. Survival was rather high (34–88%) with variations between ponds. No significant difference in survival was found between...

  3. Post-translational modifications of host proteins by Legionella pneumophila: a sophisticated survival strategy.

    Science.gov (United States)

    Rolando, Monica; Buchrieser, Carmen

    2012-03-01

    Eukaryotic proteins are tightly regulated by post-translational modifications, leading to a very subtle degree of regulation in time and space. Pathogen-mediated post-translational modifications are key strategies to modulate host factors by targeting central signaling pathways in the host cell. Legionella pneumophila, an intracellular pathogen that coevolved with protozoan hosts, encodes a large arsenal of secreted effectors conferring the ability to evade host cellular defenses and to manipulate them to promote invasion and intracellular replication. Conservation of many signaling pathways of protozoa in human macrophages confers the ability of L. pneumophila to infect humans, causing a severe pneumonia called legionnaires' disease. Most of the secreted proteins are delivered by the Dot/Icm type IV secretion system and several of these have been shown to act on different cellular pathways critical for infection. Moreover, multiple effectors target a single host function to orchestrate bacterial survival. In this review, we focus on those effectors in the repertoire of L. pneumophila proteins that target key cellular pathways by specific post-translational modifications.

  4. The Survival of Motor Neuron Protein Acts as a Molecular Chaperone for mRNP Assembly

    Directory of Open Access Journals (Sweden)

    Paul G. Donlin-Asp

    2017-02-01

    Full Text Available Spinal muscular atrophy (SMA is a motor neuron disease caused by reduced levels of the survival of motor neuron (SMN protein. SMN is part of a multiprotein complex that facilitates the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs. SMN has also been found to associate with mRNA-binding proteins, but the nature of this association was unknown. Here, we have employed a combination of biochemical and advanced imaging methods to demonstrate that SMN promotes the molecular interaction between IMP1 protein and the 3′ UTR zipcode region of β-actin mRNA, leading to assembly of messenger ribonucleoprotein (mRNP complexes that associate with the cytoskeleton to facilitate trafficking. We have identified defects in mRNP assembly in cells and tissues from SMA disease models and patients that depend on the SMN Tudor domain and explain the observed deficiency in mRNA localization and local translation, providing insight into SMA pathogenesis as a ribonucleoprotein (RNP-assembly disorder.

  5. Comparative characteristic of the methods of protein antigens epitope mapping

    Directory of Open Access Journals (Sweden)

    O. Yu. Galkin

    2014-08-01

    Full Text Available Comparative analysis of experimental methods of epitope mapping of protein antigens has been carried out. The vast majority of known techniques are involved in immunochemical study of the interaction of protein molecules or peptides with antibodies of corresponding specifici­ty. The most effective and widely applicable metho­dological techniques are those that use synthetic and genetically engineered peptides. Over the past 30 years, these groups of methods have travelled a notable evolutionary path up to the maximum automation and the detection of antigenic determinants of various types (linear and conformational epitopes, and mimotopes. Most of epitope searching algorithms were integrated into a computer program, which greatly facilitates the analysis of experimental data and makes it possible to create spatial models. It is possible to use comparative epitope mapping for solving the applied problems; this less time-consuming method is based on the analysis of competition between different antibodies interactions with the same antigen. The physical method of antigenic structure study is X-ray analysis of antigen-antibody complexes, which may be applied only to crystallizing­ proteins, and nuclear magnetic resonance.

  6. Comparative analyses of longevity and senescence reveal variable survival benefits of living in zoos across mammals.

    Science.gov (United States)

    Tidière, Morgane; Gaillard, Jean-Michel; Berger, Vérane; Müller, Dennis W H; Bingaman Lackey, Laurie; Gimenez, Olivier; Clauss, Marcus; Lemaître, Jean-François

    2016-11-07

    While it is commonly believed that animals live longer in zoos than in the wild, this assumption has rarely been tested. We compared four survival metrics (longevity, baseline mortality, onset of senescence and rate of senescence) between both sexes of free-ranging and zoo populations of more than 50 mammal species. We found that mammals from zoo populations generally lived longer than their wild counterparts (84% of species). The effect was most notable in species with a faster pace of life (i.e. a short life span, high reproductive rate and high mortality in the wild) because zoos evidently offer protection against a number of relevant conditions like predation, intraspecific competition and diseases. Species with a slower pace of life (i.e. a long life span, low reproduction rate and low mortality in the wild) benefit less from captivity in terms of longevity; in such species, there is probably less potential for a reduction in mortality. These findings provide a first general explanation about the different magnitude of zoo environment benefits among mammalian species, and thereby highlight the effort that is needed to improve captive conditions for slow-living species that are particularly susceptible to extinction in the wild.

  7. Inhibition of the Mitochondrial Fission Protein Drp1 Improves Survival in a Murine Cardiac Arrest Model

    Science.gov (United States)

    Sharp, Willard W.; Beiser, David G.; Fang, Yong Hu; Han, Mei; Piao, Lin; Varughese, Justin; Archer, Stephen L.

    2015-01-01

    Objectives Survival following sudden cardiac arrest is poor despite advances in cardiopulmonary resuscitation (CPR) and the use of therapeutic hypothermia. Dynamin related protein 1 (Drp1), a regulator of mitochondrial fission, is an important determinant of reactive oxygen species generation, myocardial necrosis, and left ventricular function following ischemia/reperfusion injury, but its role in cardiac arrest is unknown. We hypothesized that Drp1 inhibition would improve survival, cardiac hemodynamics, and mitochondrial function in an in vivo model of cardiac arrest. Design Laboratory investigation. Setting University laboratory Interventions Anesthetized and ventilated adult female C57BL/6 wild-type mice underwent an 8-min KCl induced cardiac arrest followed by 90 seconds of CPR. Mice were then blindly randomized to a single intravenous injection of Mdivi-1 (0.24 mg/kg), a small molecule Drp1 inhibitor or vehicle (DMSO). Measurements and Main Results Following resuscitation from cardiac arrest, mitochondrial fission was evidenced by Drp1 translocation to the mitochondrial membrane and a decrease in mitochondrial size. Mitochondrial fission was associated with increased lactate and evidence of oxidative damage. Mdivi-1 administration during CPR inhibited Drp1 activation, preserved mitochondrial morphology, and decreased oxidative damage. Mdivi-1 also reduced the time to return of spontaneous circulation (ROSC) 116±4 vs. 143±7 sec (pcardiac arrest. Conclusions Post cardiac arrest inhibition of Drp1 improves time to ROSC and myocardial hemodynamics resulting in improved survival and neurological outcomes in a murine model of cardiac arrest. Pharmacological targeting of mitochondrial fission may be a promising therapy for cardiac arrest. PMID:25599491

  8. Outer surface protein B is critical for Borrelia burgdorferi adherence and survival within Ixodes ticks.

    Directory of Open Access Journals (Sweden)

    Girish Neelakanta

    2007-03-01

    Full Text Available Survival of Borrelia burgdorferi in ticks and mammals is facilitated, at least in part, by the selective expression of lipoproteins. Outer surface protein (Osp A participates in spirochete adherence to the tick gut. As ospB is expressed on a bicistronic operon with ospA, we have now investigated the role of OspB by generating an OspB-deficient B. burgdorferi and examining its phenotype throughout the spirochete life cycle. Similar to wild-type isolates, the OspB-deficient B. burgdorferi were able to readily infect and persist in mice. OspB-deficient B. burgdorferi were capable of migrating to the feeding ticks but had an impaired ability to adhere to the tick gut and survive within the vector. Furthermore, the OspB-deficient B. burgdorferi bound poorly to tick gut extracts. The complementation of the OspB-deficient spirochete in trans, with a wild-type copy of ospB gene, restored its ability to bind tick gut. Taken together, these data suggest that OspB has an important role within Ixodes scapularis and that B. burgdorferi relies upon multiple genes to efficiently persist in ticks.

  9. Comparing protein VEGF inhibitors: In vitro biological studies

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Lanlan; Liang, Xiao Huan [Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080 (United States); Ferrara, Napoleone, E-mail: nf@gene.com [Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080 (United States)

    2011-05-06

    Highlights: {yields} VEGF is a mediator of angiogenesis. {yields} VEGF inhibitors have clinical applications in cancer and eye disorders. {yields} Five protein VEGF inhibitors were compared for their ability to inhibit. {yields} VEGF-induced activities in cultured endothelial cells. -- Abstract: VEGF inhibitors are widely used as a therapy for tumors and intravascular neovascular disorders, but limited and conflicting data regarding their relative biological potencies are available. The purpose of the study is to compare different protein VEGF inhibitors for their ability to inhibit VEGF-stimulated activities. We tested ranibizumab, the full-length variant of ranibizumab (Mab Y0317), bevacizumab, the VEGF-TrapR1R2 and Flt(1-3)-IgG in bioassays measuring VEGF-stimulated proliferation of bovine retinal microvascular endothelial cells or chemotaxis of human umbilical vein endothelial cells (HUVEC). The inhibitors were also compared for their ability to inhibit MAP kinase activation in HUVECs following VEGF addition. Ranibizumab, VEGF-TrapR1R2 and Flt(1-3)-IgG had very similar potencies in the bioassays tested. Bevacizumab was over 10-fold less potent than these molecules. Mab Y0317 was over 30-fold more potent than bevacizumab. The findings reported in this manuscript describe important intrinsic characteristics of several VEGF inhibitors that may be useful to design and interpret preclinical or clinical studies.

  10. The aminoglycoside multi-acetylating activity of the enhanced intracellular survival (Eis) protein from Mycobacterium smegmatis and its inhibition

    OpenAIRE

    Chen, Wenjing; Green, Keith D.; Tsodikov, Oleg V.; Garneau-Tsodikova, Sylvie

    2012-01-01

    The enhanced intracellular survival (Eis) protein improves Mycobacterium smegmatis (Msm) survival in macrophages and functions as the acetyltransferase responsible for kanamycin A resistance, a hallmark of extensively drug-resistant (XDR) tuberculosis, in a large number of Mycobacterium tuberculosis (Mtb) clinical isolates. We recently demonstrated that Eis from Mtb (Eis_Mtb) efficiently multi-acetylates a variety of aminoglycoside (AG) antibiotics. Here, to gain insight into the origin of su...

  11. Effect of a long-term high-protein diet on survival, obesity development, and gut microbiota in mice

    DEFF Research Database (Denmark)

    Kiilerich, Pia; Myrmel, Lene Secher; Fjære, Even

    2016-01-01

    , affecting pathways related to metabolism and inflammation. Analysis of fecal bacterial DNA using the Mouse Intestinal Tract Chip revealed significant changes in the composition of the gut microbiota in relation to host age and dietary fat content, but not the protein/sucrose ratio. Accordingly, dietary fat......Female C57BL/6J mice were fed a regular low-fat diet or high-fat diets combined with either high or low protein-to-sucrose ratios during their entire lifespan to examine the long-term effects on obesity development, gut microbiota, and survival. Intake of a high-fat diet with a low protein...... rather than the protein/sucrose ratio or adiposity is a major driver shaping the gut microbiota, whereas the effect of a high-fat diet on survival is dependent on the protein/sucrose ratio....

  12. Breast Milk from Smokers Contains Less Cholesterol and Protein and Smaller Size of Apolipoprotein A-I Resulting in Lower Zebrafish Embryo Survivability.

    Science.gov (United States)

    Kim, Seong-Min; Kim, Suk-Jeong; Kim, Jae-Yong; Kim, Jae-Ryong; Cho, Kyung-Hyun

    To determine the quality of breast milk (BM), we compared the functions of BM from ex-smokers and nonsmokers. We analyzed the contents of lipids, glucose, and protein in BM from ex-smokers (10 cigarettes/day for 13 ± 3 years) as well as infant formula. Nonsmokers' BM showed 2.4- and 1.4-fold higher cholesterol and protein contents, respectively, than BM from smokers. Infant formula contained almost no cholesterol, but did show remarkably higher glucose and triglyceride levels than BM. Microinjection of BM (50 nL) from nonsmokers and smokers into zebrafish embryos resulted in 59% and 44% survival, respectively, whereas formula injection resulted in 31% survival. The higher cholesterol and protein contents of BM were directly correlated with higher embryo survivability, suggesting that cholesterol content is directly and critically associated with growth of neonate infants. Smokers' BM contained smaller-sized apolipoproteinA-I (apoA-I) (24.4 ± 0.2 kDa) than BM from nonsmokers (26.7 ± 0.4 kDa), suggesting that putative modification and cleavage occurred in apoA-I. BM containing higher molecular weight apoA-I resulted in higher embryo survivability. Smoking before pregnancy can affect the composition and quality of BM, resulting in almost complete loss of cholesterol and protein, especially lactoferrin, lactalbumin, and apoA-I, accompanied by proteolytic degradation. These impairment effects of BM are associated with elevation of oxidative stress and lower embryo survivability.

  13. Survival Strategies of Yeast and Filamentous Fungi against the Antifungal Protein AFP*

    Science.gov (United States)

    Ouedraogo, Jean Paul; Hagen, Silke; Spielvogel, Anja; Engelhardt, Susanne; Meyer, Vera

    2011-01-01

    The activities of signaling pathways are critical for fungi to survive antifungal attack and to maintain cell integrity. However, little is known about how fungi respond to antifungals, particularly if these interact with multiple cellular targets. The antifungal protein AFP is a very potent inhibitor of chitin synthesis and membrane integrity in filamentous fungi and has so far not been reported to interfere with the viability of yeast strains. With the hypothesis that the susceptibility of fungi toward AFP is not merely dependent on the presence of an AFP-specific target at the cell surface but relies also on the cell's capacity to counteract AFP, we used a genetic approach to decipher defense strategies of the naturally AFP-resistant strain Saccharomyces cerevisiae. The screening of selected strains from the yeast genomic deletion collection for AFP-sensitive phenotypes revealed that a concerted action of calcium signaling, TOR signaling, cAMP-protein kinase A signaling, and cell wall integrity signaling is likely to safeguard S. cerevisiae against AFP. Our studies uncovered that the yeast cell wall gets fortified with chitin to defend against AFP and that this response is largely dependent on calcium/Crz1p signaling. Most importantly, we observed that stimulation of chitin synthesis is characteristic for AFP-resistant fungi but not for AFP-sensitive fungi, suggesting that this response is a successful strategy to protect against AFP. We finally propose the adoption of the damage-response framework of microbial pathogenesis for the interactions of antimicrobial proteins and microorganisms in order to comprehensively understand the outcome of an antifungal attack. PMID:21343301

  14. Comparative survival rates of oriental fruit moth (Lepidoptera: Tortricidae) larvae on shoots and fruit of apple and peach.

    Science.gov (United States)

    Myers, Clayton T; Hull, Larry A; Krawczyk, Grzegorz

    2006-08-01

    Studies were designed to examine the effects of host plants on oriental fruit moth, Grapholita molesta (Busck) (Lepidoptera: Tortricidae), survival. G. molesta larval survival in the orchard was comparable between apple (Malus spp.) and peach (Prunus spp.) shoots, indicating that both host species can harbor large larval populations during the early season. G. molesta larvae used multiple shoots for feeding and development on peaches but usually only damaged single shoots in apple. Survival differences were present between peach and apple fruit, but this survival was affected by fruit maturity level. Generally, larval survival higher was in ripening peach fruit than in green, immature apple fruit. Larval survival varied among several apple cultivars, indicating that cultivar-level variability needs to be considered. These host-associated effects may impact efforts to predictively model G. molesta populations in commercial orchards where multiple host plant species, or different cultivars of the same species are often grown in proximity. Thus, host-associated dynamics should be included into future population models that underlie management programs.

  15. Less extensive surgery compared to extensive surgery: survival seems similar in young women with adult ovarian granulosa cell tumor.

    Science.gov (United States)

    Lauszus, Finn F; Petersen, Astrid C; Neumann, Gudrun; Cleemann, Line; Rosgaard, Anni; Jørgensen, Annemette; Vandborg, Mai; Jakobsen, Anders

    2014-06-01

    To describe the outcome of adult granulosa cell tumor (AGCT) with respect to initial clinical findings, methods of surgery, and perioperative treatment. Retrospective follow-up study. All hospitals in Jutland. 163 women diagnosed with AGCT. Follow-up by hospital data files, general practitioner, death certificate, and autopsy report. Revision of histopathology by a single pathologist. Survival and relapse by clinical data, stage, and type of surgery. The incidence of AGCT was 1.37 per year per 100,000 women (95% CI: 1.08, 1.68). The median follow-up time was 15 years and for the 79 surviving women 22 years. Stage I was found in 94% of cases. Relapse occurred in 24% of women in stage I and 100% of the other stages. Survival in stage I was 95%, 89% and 84% after 5, 10 and 20 years respectively. Increased survival of stage I in postmenopausal women was associated with surgery including hysterectomy and bilateral oophorectomy (ptumor. Age and type of surgery, besides stage, influenced survival. Total abdominal hysterectomy and bilateral salpingo-oophorectomy is the recommended treatment with advancing age. At younger age less extensive surgery was associated with similar survival compared to extensive surgery, but with advancing age conservative surgery increased the risk of relapse and death. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  16. An Incident Cohort Study Comparing Survival on Home Hemodialysis and Peritoneal Dialysis (Australia and New Zealand Dialysis and Transplantation Registry)

    Science.gov (United States)

    Nadeau-Fredette, Annie-Claire; Hawley, Carmel M.; Pascoe, Elaine M.; Chan, Christopher T.; Clayton, Philip A.; Polkinghorne, Kevan R.; Boudville, Neil; Leblanc, Martine

    2015-01-01

    Background and objectives Home dialysis is often recognized as a first-choice therapy for patients initiating dialysis. However, studies comparing clinical outcomes between peritoneal dialysis and home hemodialysis have been very limited. Design, setting, participants, & measurements This Australia and New Zealand Dialysis and Transplantation Registry study assessed all Australian and New Zealand adult patients receiving home dialysis on day 90 after initiation of RRT between 2000 and 2012. The primary outcome was overall survival. The secondary outcomes were on-treatment survival, patient and technique survival, and death-censored technique survival. All results were adjusted with three prespecified models: multivariable Cox proportional hazards model (main model), propensity score quintile–stratified model, and propensity score–matched model. Results The study included 10,710 patients on incident peritoneal dialysis and 706 patients on incident home hemodialysis. Treatment with home hemodialysis was associated with better patient survival than treatment with peritoneal dialysis (5-year survival: 85% versus 44%, respectively; log-rank Pdialysis. PMID:26068181

  17. Survival to different acid challenges and outer membrane protein profiles of pathogenic Escherichia coli strains isolated from pozol, a Mexican typical maize fermented food.

    Science.gov (United States)

    Sainz, Teresita; Pérez, Julia; Villaseca, Jorge; Hernández, Ulises; Eslava, Carlos; Mendoza, Guillermo; Wacher, Carmen

    2005-12-15

    In this study, the acid resistance and the changes in outer membrane protein (Omps) profiles of Escherichia coli strains isolated from pozol, an acid-fermented maize beverage consumed in Southeastern Mexico, were determined. Results showed that adaptation to acid by these E. coli strains significantly enhances their survival in acid conditions. Changes in Omp profiles were found in non-adapted acid challenged cells compared with non-challenged cells that had not been adapted to acid. Challenged adapted cells showed no significant changes in these profiles when compared with the acid adapted non-challenged strains. N-terminal sequences of some of the Omps were determined. The intensity of the main porins OmpC and OmpA was lower in the acid challenged strains, than in the non-challenged ones. The OmpF porin was identified in non-challenged K12 strain, but did not appear in adapted or non-adapted pozol strains nor in E. coli O157:H7. A protein band with an approximate molecular mass of 22 kDa corresponds to OmpW and its expression decreased in pozol strains challenged with HCl and lactic acid. OmpX was one of the main proteins expressed when strains were acid challenged with organic acids. Seventy out of seventy-three E. coli strains isolated from pozol in a previous work [Sainz, T., Wacher, C., Espinoza, J., Centurion, D., Navarro, A., Molina, J., Cravioto, A., Eslava, C., 2001. Survival and characterization of Escherichia coli strains in a typical Mexican acid-fermented food. International Journal of Food Microbiology 71, 169-176] carry this gene and belong to a reported pathogenic class of E. coli strains, or have virulence factors or survived at pH values less than 4.8. We suggest this protein could be involved in survival to stress conditions.

  18. Comparative analyses of nonpathogenic, opportunistic, and totally pathogenic mycobacteria reveal genomic and biochemical variabilities and highlight the survival attributes of Mycobacterium tuberculosis.

    Science.gov (United States)

    Rahman, Syed Asad; Singh, Yadvir; Kohli, Sakshi; Ahmad, Javeed; Ehtesham, Nasreen Z; Tyagi, Anil K; Hasnain, Seyed E

    2014-11-04

    Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition. Our comparative genome size analysis of 44 mycobacterial genomes revealed that the nonpathogenic (NP) genomes were bigger than those of opportunistic (OP) or totally pathogenic (TP) mycobacteria, with the TP genomes being smaller yet variable in size--their genomic plasticity reflected their ability to evolve and survive under various environmental conditions. From the 44 mycobacterial species, 13 species, representing TP, OP, and NP, were selected for genomic-relatedness analyses. Analysis of homologous protein-coding genes shared between Mycobacterium indicus pranii (NP), Mycobacterium intracellulare ATCC 13950 (OP), and Mycobacterium tuberculosis H37Rv (TP) revealed that 4,995 (i.e., ~95%) M. indicaus pranii proteins have homology with M. intracellulare, whereas the homologies among M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv were significantly lower. A total of 4,153 (~79%) M. indicus pranii proteins and 4,093 (~79%) M. intracellulare ATCC 13950 proteins exhibited homology with the M. tuberculosis H37Rv proteome, while 3,301 (~82%) and 3,295 (~82%) M. tuberculosis H37Rv proteins showed homology with M. indicus pranii and M. intracellulare ATCC 13950 proteomes, respectively. Comparative metabolic pathway analyses of TP/OP/NP mycobacteria showed enzymatic plasticity between M. indicus pranii (NP) and M. intracellulare ATCC 13950 (OP), Mycobacterium avium 104 (OP), and M. tuberculosis H37Rv (TP). Mycobacterium tuberculosis seems to have acquired novel alternate pathways with possible roles in metabolism, host-pathogen interactions, virulence, and intracellular survival, and by implication some of these could be potential drug targets. The complete sequence analysis of Mycobacterium indicus pranii, a novel species of Mycobacterium shown earlier to have strong immunomodulatory properties and currently in use for

  19. Interval breast cancers have worse tumor characteristics and survival compared to screen-detected breast cancers

    NARCIS (Netherlands)

    de Munck, L.; Siesling, S.; Pijnappel, R. M.; van der Vegt, B.; de Bock, G. H.

    2016-01-01

    Background There is debate to what extend screen-detected cancers (SDC) differ in tumor characteristics and survival from tumors that are detected not trough screening. These can be divide into three groups. Firstly, tumors who manifest clinically in the period between two screens after a negative

  20. Effect of a long-term high-protein diet on survival, obesity development, and gut microbiota in mice

    NARCIS (Netherlands)

    Kiilerich, Pia; Myrmel, Lene Secher; Fjære, Even; Hao, Qin; Hugenholtz, Floor; Sonne, Si Brask; Derrien, Muriel; Pedersen, Lone Møller; Petersen, Rasmus Koefoed; Mortensen, Alicja; Licht, Tine Rask; Rømer, Maria Unni; Vogel, Ulla Birgitte; Waagbø, Linn Jeanette; Giallourou, Natasa; Feng, Qiang; Xiao, Liang; Liu, Chuan; Liaset, Bjørn; Kleerebezem, Michiel; Wang, Jun; Madsen, Lise; Kristiansen, Karsten

    2016-01-01

    Female C57BL/6J mice were fed a regular low-fat diet or high-fat diets combined with either high or low protein-to-sucrose ratios during their entire lifespan to examine the long-term effects on obesity development, gut microbiota, and survival. Intake of a high-fat diet with a low

  1. Effect of a long-term high-protein diet on survival, obesity development, and gut microbiota in mice

    DEFF Research Database (Denmark)

    Kiilerich, Pia; Myrmel, Lene Secher; Fjære, Even

    2016-01-01

    Female C57BL/6J mice were fed a regular low-fat diet or high-fat diets combined with either high or low protein-to-sucrose ratios during their entire lifespan to examine the long-term effects on obesity development, gut microbiota, and survival. Intake of a high-fat diet with a low protein....../sucrose ratio precipitated obesity and reduced survival relative to mice fed a low-fat diet. By contrast, intake of a high-fat diet with a high protein/sucrose ratio attenuated lifelong weight gain and adipose tissue expansion, and survival was not significantly altered relative to low-fat-fed mice. Our...... findings support the notion that reduced survival in response to high-fat/high-sucrose feeding is linked to obesity development. Digital gene expression analyses, further validated by qPCR, demonstrated that the protein/sucrose ratio modulated global gene expression over time in liver and adipose tissue...

  2. Retinoblastoma protein controls growth, survival and neuronal migration in human cerebral organoids.

    Science.gov (United States)

    Matsui, Takeshi; Nieto-Estévez, Vanesa; Kyrychenko, Sergii; Schneider, Jay W; Hsieh, Jenny

    2017-03-15

    The tumor suppressor retinoblastoma protein (RB) regulates S-phase cell cycle entry via E2F transcription factors. Knockout (KO) mice have shown that RB plays roles in cell migration, differentiation and apoptosis, in developing and adult brain. In addition, the RB family is required for self-renewal and survival of human embryonic stem cells (hESCs). Since little is known about the role of RB in human brain development, we investigated its function in cerebral organoids differentiated from gene-edited hESCs lacking RB. We show that RB is abundantly expressed in neural stem and progenitor cells in organoids at 15 and 28 days of culture. RB loss promoted S-phase entry in DCX + cells and increased apoptosis in Sox2 + neural stem and progenitor cells, and in DCX + and Tuj1 + neurons. Associated with these cell cycle and pro-apoptotic effects, we observed increased CCNA2 and BAX gene expression, respectively. Moreover, we observed aberrant Tuj1 + neuronal migration in RB-KO organoids and upregulation of the gene encoding VLDLR, a receptor important in reelin signaling. Corroborating the results in RB-KO organoids in vitro , we observed ectopically localized Tuj1 + cells in RB-KO teratomas grown in vivo Taken together, these results identify crucial functions for RB in the cerebral organoid model of human brain development. © 2017. Published by The Company of Biologists Ltd.

  3. Identification of cytoskeleton-associated proteins essential for lysosomal stability and survival of human cancer cells

    DEFF Research Database (Denmark)

    Groth-Pedersen, Line; Aits, Sonja; Corcelle-Termeau, Elisabeth

    2012-01-01

    Microtubule-disturbing drugs inhibit lysosomal trafficking and induce lysosomal membrane permeabilization followed by cathepsin-dependent cell death. To identify specific trafficking-related proteins that control cell survival and lysosomal stability, we screened a molecular motor siRNA library...... in human MCF7 breast cancer cells. SiRNAs targeting four kinesins (KIF11/Eg5, KIF20A, KIF21A, KIF25), myosin 1G (MYO1G), myosin heavy chain 1 (MYH1) and tropomyosin 2 (TPM2) were identified as effective inducers of non-apoptotic cell death. The cell death induced by KIF11, KIF21A, KIF25, MYH1 or TPM2 si......), increased dextran accumulation (KIF20A), or reduced autophagic flux (MYO1G, MYH1). Importantly, all seven siRNAs also killed human cervix cancer (HeLa) and osteosarcoma (U-2-OS) cells and sensitized cancer cells to other lysosome-destabilizing treatments, i.e. photo-oxidation, siramesine, etoposide...

  4. Comparing the survival rate of juvenile Chinook salmon migrating through hydropower systems using injectable and surgical acoustic transmitters

    Science.gov (United States)

    Deng, Z. D.; Martinez, J. J.; Li, H.; Harnish, R. A.; Woodley, C. M.; Hughes, J. A.; Li, X.; Fu, T.; Lu, J.; McMichael, G. A.; Weiland, M. A.; Eppard, M. B.; Skalski, J. R.; Townsend, R. L.

    2017-02-01

    Acoustic telemetry is one of the primary technologies for studying the behavior and survival of fishes throughout the world. The size and performance of the transmitter are key limiting factors. The newly developed injectable transmitter is the first acoustic transmitter that can be implanted via injection instead of surgery. A two-part field study was conducted to evaluate the performance of the injectable transmitter and its effect on the survival of implanted fish. The injectable transmitter performed well and similarly to the proceeding generation of commercially-available JSATS transmitters tested concurrently. Snake River subyearling Chinook salmon smolts implanted with the injectable transmitter had a higher survival probability from release to each of eleven downstream detection arrays, because reach-specific survival estimates were significantly higher for the injectable group in three of the eleven reaches examined. Overall, the injectable group had a 0.263 (SE = 0.017) survival probability over the entire 500 km study area compared to 0.199 (0.012) for the surgically implanted group. The reduction in size and ability to implant the new transmitter via injection has reduced the tag or tagging effect bias associated with studying small fishes. The information gathered with this new technology is helping to evaluate the impacts of dams on fishes.

  5. The cytoprotective protein clusterin is overexpressed in hypergastrinemic rodent models of oxyntic preneoplasia and promotes gastric cancer cell survival.

    Directory of Open Access Journals (Sweden)

    Pål Vange

    Full Text Available The cytoprotective protein clusterin is often dysregulated during tumorigenesis, and in the stomach, upregulation of clusterin marks emergence of the oxyntic atrophy (loss of acid-producing parietal cells-associated spasmolytic polypeptide-expressing metaplasia (SPEM. The hormone gastrin is important for normal function and maturation of the gastric oxyntic mucosa and hypergastrinemia might be involved in gastric carcinogenesis. Gastrin induces expression of clusterin in adenocarcinoma cells. In the present study, we examined the expression patterns and gastrin-mediated regulation of clusterin in gastric tissue from: humans; rats treated with proton pump (H+/K+-ATPase inhibitors and/or a gastrin receptor (CCK2R antagonist; H+/K+-ATPase β-subunit knockout (H/K-β KO mice; and Mongolian gerbils infected with Helicobacter pylori and given a CCK2R antagonist. Biological function of secretory clusterin was studied in human gastric cancer cells. Clusterin was highly expressed in neuroendocrine cells in normal oxyntic mucosa of humans and rodents. In response to hypergastrinemia, expression of clusterin increased significantly and its localization shifted to basal groups of proliferative cells in the mucous neck cell-chief cell lineage in all animal models. That shift was partially inhibited by antagonizing the CCK2R in rats and gerbils. The oxyntic mucosa of H/K-β KO mice contained areas with clusterin-positive mucous cells resembling SPEM. In gastric adenocarcinomas, clusterin mRNA expression was higher in diffuse tumors containing signet ring cells compared with diffuse tumors without signet ring cells, and clusterin seemed to be secreted by tumor cells. In gastric cancer cell lines, gastrin increased secretion of clusterin, and both gastrin and secretory clusterin promoted survival after starvation- and chemotherapy-induced stress. Overall, our results indicate that clusterin is overexpressed in hypergastrinemic rodent models of oxyntic

  6. Extracellular administration of BCL2 protein reduces apoptosis and improves survival in a murine model of sepsis.

    Directory of Open Access Journals (Sweden)

    Akiko Iwata

    2011-02-01

    Full Text Available Severe sepsis and septic shock are major causes of morbidity and mortality worldwide. In experimental sepsis there is prominent apoptosis of various cell types, and genetic manipulation of death and survival pathways has been shown to modulate organ injury and survival.We investigated the effect of extracellular administration of two anti-apoptotic members of the BCL2 (B-cell lymphoma 2 family of intracellular regulators of cell death in a murine model of sepsis induced by cecal ligation and puncture (CLP. We show that intraperitoneal injection of picomole range doses of recombinant human (rh BCL2 or rhBCL2A1 protein markedly improved survival as assessed by surrogate markers of death. Treatment with rhBCL2 or rhBCL2A1 protein significantly reduced the number of apoptotic cells in the intestine and heart following CLP, and this was accompanied by increased expression of endogenous mouse BCL2 protein. Further, mice treated with rhBCL2A1 protein showed an increase in the total number of neutrophils in the peritoneum following CLP with reduced neutrophil apoptosis. Finally, although neither BCL2 nor BCL2A1 are a direct TLR2 ligand, TLR2-null mice were not protected by rhBCL2A1 protein, indicating that TLR2 signaling was required for the protective activity of extracellularly adminsitered BCL2A1 protein in vivo.Treatment with rhBCL2A1 or rhBCL2 protein protects mice from sepsis by reducing apoptosis in multiple target tissues, demonstrating an unexpected, potent activity of extracellularly administered BCL2 BH4-domain proteins.

  7. Comparative characteristics of spermatozoa harvested and cryopreserved in culture and cryoprotectant media with or without donor serum proteins.

    Science.gov (United States)

    Ata'Allah, Ghofraan A; Adenan, Noor Azmi Mat; Razali, Nuguelis; Palaniappan, Kannappan; Saad, Rosliza; Idris, Siti Khadijah; Kanniah, Krishnan; Ali, Jaffar

    2017-06-01

    The objectives of this study is to evaluate the efficacy of protein-free media in the preparation, holding and crypreservation of spermatazoa for use in ART. Normozoospermic semen samples (N=71) were used to compare the effects of media on the survival and quality of spermatozoa when washed and cultured with different media with and without added proteins at 4°C, 15°C, 22°C and 37°C for 0, 4-7 and 24h. Survival and quality of spermatozoa were assessed after freeze-thaw with synthetic cryoprotectant with and without proteins. Ethics/IRB approval was obtained (Ref. 1073.52). Spermatozoa parameters were similar in all media after washing and culture for 24h. Post-thaw survival and quality of spermatozoa was not significantly different 24h after thawing of samples frozen in all cryoprotectant medium. In conclusion synthetic protein-free culture and cryoprotectant media are equal in efficacy to protein-containing media in culture and cryopreservation of spermatozoa . Use of these synthetic media are anticipated to significantly reduce the risk, potentially associated with conventional protein-containing media, of transmission of disease and possibly harmful undeclared proteins to the patient, baby and the healtcare worker. Synthetic media also ensure consistency of quality between batches of media. Copyright © 2017 Society for Biology of Reproduction & the Institute of Animal Reproduction and Food Research of Polish Academy of Sciences in Olsztyn. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

  8. Comparing population patterns to processes: abundance and survival of a forest salamander following habitat degradation.

    Directory of Open Access Journals (Sweden)

    Clint R V Otto

    Full Text Available Habitat degradation resulting from anthropogenic activities poses immediate and prolonged threats to biodiversity, particularly among declining amphibians. Many studies infer amphibian response to habitat degradation by correlating patterns in species occupancy or abundance with environmental effects, often without regard to the demographic processes underlying these patterns. We evaluated how retention of vertical green trees (CANOPY and coarse woody debris (CWD influenced terrestrial salamander abundance and apparent survival in recently clearcut forests. Estimated abundance of unmarked salamanders was positively related to CANOPY (β Canopy  = 0.21 (0.02-1.19; 95% CI, but not CWD (β CWD  = 0.11 (-0.13-0.35 within 3,600 m2 sites, whereas estimated abundance of unmarked salamanders was not related to CANOPY (β Canopy  = -0.01 (-0.21-0.18 or CWD (β CWD  = -0.02 (-0.23-0.19 for 9 m2 enclosures. In contrast, apparent survival of marked salamanders within our enclosures over 1 month was positively influenced by both CANOPY and CWD retention (β Canopy  = 0.73 (0.27-1.19; 95% CI and β CWD  = 1.01 (0.53-1.50. Our results indicate that environmental correlates to abundance are scale dependent reflecting habitat selection processes and organism movements after a habitat disturbance event. Our study also provides a cautionary example of how scientific inference is conditional on the response variable(s, and scale(s of measure chosen by the investigator, which can have important implications for species conservation and management. Our research highlights the need for joint evaluation of population state variables, such as abundance, and population-level process, such as survival, when assessing anthropogenic impacts on forest biodiversity.

  9. Control of mitochondrial pH by uncoupling protein 4 in astrocytes promotes neuronal survival

    KAUST Repository

    Lambert, Hélène Perreten

    2014-09-18

    Brain activity is energetically costly and requires a steady and highly regulated flow of energy equivalents between neural cells. It is believed that a substantial share of cerebral glucose, the major source of energy of the brain, will preferentially be metabolized in astrocytes via aerobic glycolysis. The aim of this study was to evaluate whether uncoupling proteins (UCPs), located in the inner membrane of mitochondria, play a role in setting up the metabolic response pattern of astrocytes. UCPs are believed to mediate the transmembrane transfer of protons, resulting in the uncoupling of oxidative phosphorylation from ATP production. UCPs are therefore potentially important regulators of energy fluxes. The main UCP isoforms expressed in the brain are UCP2, UCP4, and UCP5. We examined in particular the role of UCP4 in neuron-astrocyte metabolic coupling and measured a range of functional metabolic parameters including mitochondrial electrical potential and pH, reactive oxygen species production, NAD/NADH ratio, ATP/ADP ratio, CO2 and lactate production, and oxygen consumption rate. In brief, we found that UCP4 regulates the intramitochondrial pH of astrocytes, which acidifies as a consequence of glutamate uptake, with the main consequence of reducing efficiency of mitochondrial ATP production. The diminished ATP production is effectively compensated by enhancement of glycolysis. This nonoxidative production of energy is not associated with deleterious H2O2 production. We show that astrocytes expressing more UCP4 produced more lactate, which is used as an energy source by neurons, and had the ability to enhance neuronal survival.

  10. Molecular determinants of survival motor neuron (SMN protein cleavage by the calcium-activated protease, calpain.

    Directory of Open Access Journals (Sweden)

    Jennifer L Fuentes

    2010-12-01

    Full Text Available Spinal muscular atrophy (SMA is a leading genetic cause of childhood mortality, caused by reduced levels of survival motor neuron (SMN protein. SMN functions as part of a large complex in the biogenesis of small nuclear ribonucleoproteins (snRNPs. It is not clear if defects in snRNP biogenesis cause SMA or if loss of some tissue-specific function causes disease. We recently demonstrated that the SMN complex localizes to the Z-discs of skeletal and cardiac muscle sarcomeres, and that SMN is a proteolytic target of calpain. Calpains are implicated in muscle and neurodegenerative disorders, although their relationship to SMA is unclear. Using mass spectrometry, we identified two adjacent calpain cleavage sites in SMN, S192 and F193. Deletion of small motifs in the region surrounding these sites inhibited cleavage. Patient-derived SMA mutations within SMN reduced calpain cleavage. SMN(D44V, reported to impair Gemin2 binding and amino-terminal SMN association, drastically inhibited cleavage, suggesting a role for these interactions in regulating calpain cleavage. Deletion of A188, a residue mutated in SMA type I (A188S, abrogated calpain cleavage, highlighting the importance of this region. Conversely, SMA mutations that interfere with self-oligomerization of SMN, Y272C and SMNΔ7, had no effect on cleavage. Removal of the recently-identified SMN degron (Δ268-294 resulted in increased calpain sensitivity, suggesting that the C-terminus of SMN is important in dictating availability of the cleavage site. Investigation into the spatial determinants of SMN cleavage revealed that endogenous calpains can cleave cytosolic, but not nuclear, SMN. Collectively, the results provide insight into a novel aspect of the post-translation regulation of SMN.

  11. A multidisciplinary clinic approach improves survival in ALS: a comparative study of ALS in Ireland and Northern Ireland.

    Science.gov (United States)

    Rooney, James; Byrne, Susan; Heverin, Mark; Tobin, Katy; Dick, Alison; Donaghy, Colette; Hardiman, Orla

    2015-05-01

    Amyotrophic lateral sclerosis (ALS) is a progressive debilitating neurodegenerative disease, with a life expectancy of 3-5 years from first symptom. There is compelling evidence that those who attend a multidisciplinary clinic experience improved survival. The purpose of the study was to explore the survival of patients with ALS ascertained through population-based Registers in the Republic of Ireland (RoI) and Northern Ireland (NI), and to determine whether centralisation of services confers advantage compared with community-based care supported by a specialist care worker. The island of Ireland is divided into two countries, RoI and NI, each with an independent healthcare system. Both countries have population-based ALS Registers with full ascertainment. Data from all 719 incident ALS cases from Ireland and NI, diagnosed between 1 January 2005 and 31 December 2010, were used in the analysis. A survival benefit was identified for patients who attended the multidisciplinary ALS clinic in the RoI. (HR 0.59, 95% CI 0.49 to 0.71, p<0.001). This difference was preserved following multivariate analysis. A trend towards improved survival was noted for patients with ALS from NI when compared with RoI patients who did not attend a multidisciplinary clinic. Centralised multidisciplinary care confers a survival advantage for patients with ALS and is superior to devolved community-based care. We propose that multiple decision-making processes within a multidisciplinary setting lead to an enriched set of clinical encounters for the patient and carer that enhances clinical outcome. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  12. Comparative Analysis of Renal Functional Outcomes and Overall Survival of Elderly vs Nonelderly Patients Undergoing Radical Nephrectomy.

    Science.gov (United States)

    Peyton, Charles C; Rothberg, Michael B; Jiang, Victoria; Heavner, Matthew G; Hemal, Ashok K

    2017-02-01

    To evaluate changes in renal function and overall survival in elderly vs nonelderly patients undergoing radical nephrectomy (RN) for renal masses. We reviewed available records of 392 patients undergoing RN from 2008 through 2013. Patients were divided into elderly, defined as ≥70 years old (n = 110), or nonelderly (n = 282) at the time of nephrectomy. The groups were compared for perioperative characteristics, renal functional outcomes, and overall survival. Standard Student's t-tests were used for continuous variables and Fischer's exact tests for categorical comparisons. Kaplan-Meier estimate models for survival were compared using log-rank tests. Elderly patients were more likely to have comorbidities. Preoperative estimated glomerular filtration rate (GFR) of elderly patients was significantly lower (65.6 vs 77.9 mL/minute/1.73 m(2), p = 0.0002), as was GFR at discharge (47.7 vs 57.2 mL/minute/1.73 m(2), p = 0.001) and at maximum follow-up (46.8 vs 57.4 mL/minute/1.73 m(2), p = 0.001). Of the patients with GFR >60 before surgery, de novo CKD stage III progression (defined as GFR elderly and 53% nonelderly (odds ratio 2.47; 95% confidence interval 1.25-4.88; p = 0.01). Overall survival was not statistically different. When stratified for elderly and preoperative GFR Elderly patients who undergo RN have worse renal functional outcomes. Following nephrectomy, these patients are at higher risk of CKD progression than nonelderly patients. However, there does not appear to be a difference in overall survival between cohorts, even when stratified for preoperative GFR <60. These findings should be considered during preoperative decision-making.

  13. Flexible survival strategies of Pseudomonas aeruginosa in biofilms result in increased fitness compared with Candida albicans.

    Science.gov (United States)

    Purschke, Frauke Gina; Hiller, Ekkehard; Trick, Iris; Rupp, Steffen

    2012-12-01

    The majority of microorganisms persist in nature as surface-attached communities often surrounded by an extracellular matrix, called biofilms. Most natural biofilms are not formed by a single species but by multiple species. Microorganisms not only cooperate as in some multispecies biofilms but also compete for available nutrients. The Gram-negative bacterium Pseudomonas aeruginosa and the polymorphic fungus Candida albicans are two opportunistic pathogens that are often found coexisting in a human host. Several models of mixed biofilms have been reported for these organisms showing antagonistic behavior. To investigate the interaction of P. aeruginosa and C. albicans in more detail, we analyzed the secretome of single and mixed biofilms of both organisms using MALDI-TOF MS/MS at several time points. Overall 247 individual proteins were identified, 170 originated from P. aeruginosa and 77 from C. albicans. Only 39 of the 131 in mixed biofilms identified proteins were assigned to the fungus whereby the remaining 92 proteins belonged to P. aeruginosa. In single-species biofilms, both organisms showed a higher diversity of proteins with 73 being assigned to C. albicans and 154 to P. aeruginosa. Most interestingly, P. aeruginosa in the presence of C. albicans secreted 16 proteins in significantly higher amounts or exclusively among other virulence factors such as exotoxin A and iron acquisition systems. In addition, the high affinity iron-binding siderophore pyoverdine was identified in mixed biofilms but not in bacterial biofilms, indicating that P. aeruginosa increases its capability to sequester iron in competition with C. albicans. In contrast, C. albicans metabolism was significantly reduced, including a reduction in detectable iron acquisition proteins. The results obtained in this study show that microorganisms not only compete with the host for essential nutrients but also strongly with the present microflora in order to gain a competitive advantage.

  14. Flexible Survival Strategies of Pseudomonas aeruginosa in Biofilms Result in Increased Fitness Compared with Candida albicans *

    Science.gov (United States)

    Purschke, Frauke Gina; Hiller, Ekkehard; Trick, Iris; Rupp, Steffen

    2012-01-01

    The majority of microorganisms persist in nature as surface-attached communities often surrounded by an extracellular matrix, called biofilms. Most natural biofilms are not formed by a single species but by multiple species. Microorganisms not only cooperate as in some multispecies biofilms but also compete for available nutrients. The Gram-negative bacterium Pseudomonas aeruginosa and the polymorphic fungus Candida albicans are two opportunistic pathogens that are often found coexisting in a human host. Several models of mixed biofilms have been reported for these organisms showing antagonistic behavior. To investigate the interaction of P. aeruginosa and C. albicans in more detail, we analyzed the secretome of single and mixed biofilms of both organisms using MALDI-TOF MS/MS at several time points. Overall 247 individual proteins were identified, 170 originated from P. aeruginosa and 77 from C. albicans. Only 39 of the 131 in mixed biofilms identified proteins were assigned to the fungus whereby the remaining 92 proteins belonged to P. aeruginosa. In single-species biofilms, both organisms showed a higher diversity of proteins with 73 being assigned to C. albicans and 154 to P. aeruginosa. Most interestingly, P. aeruginosa in the presence of C. albicans secreted 16 proteins in significantly higher amounts or exclusively among other virulence factors such as exotoxin A and iron acquisition systems. In addition, the high affinity iron-binding siderophore pyoverdine was identified in mixed biofilms but not in bacterial biofilms, indicating that P. aeruginosa increases its capability to sequester iron in competition with C. albicans. In contrast, C. albicans metabolism was significantly reduced, including a reduction in detectable iron acquisition proteins. The results obtained in this study show that microorganisms not only compete with the host for essential nutrients but also strongly with the present microflora in order to gain a competitive advantage. PMID

  15. Contribution of protein isoaspartate methyl transferase (PIMT) in the survival of Salmonella Typhimurium under oxidative stress and virulence.

    Science.gov (United States)

    Kumawat, Manoj; Pesingi, Pavan Kumar; Agarwal, Rajesh Kumar; Goswami, Tapas Kumar; Mahawar, Manish

    2016-06-01

    The enteric pathogen Salmonella Typhimurium (ST) survives inside the oxidative environment of phagocytic cells. Phagocyte generated oxidants primarily target proteins and modify amino acids in them. These modifications render the targeted proteins functionally inactive. Conversion of Asp to iso-Asp is one of the several known oxidant mediated amino acids modifications. By repairing iso-Asp to Asp, protein-isoaspartyl methyltransferase (PIMT) maintains the activities of proteins and thus helps in cellular survival under oxidative stress. To elucidate the role of PIMT in ST survival under oxidative stress, we have constructed a pimt gene deletion strain (Δpimt strain) of ST. The Δpimt strain grows normally in various culture media in vitro. However, in comparison to wild type ST, the Δpimt strain is found significantly (psurvival of Δpimt mutant strain against oxidants in vitro and also inside the macrophages. In mice model, the LD50 for wild type ST and mutant Δpimt has been 1.73×10(4) and 1.38×10(5), respectively. Further, the mutant strain shows reduced dissemination to spleen and liver in mice. Following infection with a mixture of wild type ST and the Δpimt mutant (co-infection experiment), we recover significantly (p<0.001) less numbers of mutant bacteria from the spleen and liver of mice. Copyright © 2016 Elsevier GmbH. All rights reserved.

  16. Comparative evaluation of protein and amino acid composition of ...

    African Journals Online (AJOL)

    The seeds of melon (Citrullus vulgaris) and water melon (Citrullus lanatus) from Nasarawa town in Nasarawa State and Shagari town in Sokoto State, Nigeria were respectively analyzed for their crude protein and amino acids contents. The crude protein compositions of the melon and water melon seeds were found to be ...

  17. Comparative study of C-Reactive Protein and other biochemical ...

    African Journals Online (AJOL)

    Serum levels of C-reactive proteins (CRP), Alanine aminotransferase (ALT), Aspartate aminotransferase (AST), total protein, albumin and globulins were investigated using high sensitivity Immunoturbidometric and colorimetric techniques in individuals with hepatitis (n=50), Malaria (n=50) and 40 control subjects in age ...

  18. Deficiency of Bid protein reduces sepsis-induced apoptosis and inflammation, while improving septic survival.

    Science.gov (United States)

    Chung, Chun-Shiang; Venet, Fabienne; Chen, Yaping; Jones, Leslie N; Wilson, Douglas C; Ayala, Carol A; Ayala, Alfred

    2010-08-01

    Increased apoptotic cell death is believed to play a pathological role in patients with sepsis and experimental animals. Apoptosis can be induced by either a cell death receptor (extrinsic) or a mitochondrial (intrinsic) pathway. Bid, a proapoptotic member of the Bcl-2 family, is thought to mediate the cross talk between the extrinsic and intrinsic pathways of apoptosis; however, little is known about the action of Bid in the development of apoptosis and organ-specific tissue damage/cell death as seen in polymicrobial sepsis. Our results show that after the onset of sepsis, tBid (the active form of Bid) is significantly increased in mitochondrial fractions of the thymus, spleen, Peyer patches, and liver, and that Fas or FasL deficiency blocks Bid activation in various tissues after septic challenge. Increased Bid activation is correlated with increased active caspase-3, caspase-9, and apoptosis during sepsis. Bid-deficient mice exhibit significantly reduced apoptosis in the thymus, spleen, and Peyer patches compared with background mice after sepsis. Furthermore, Bid-deficient mice had significantly reduced systemic and local inflammatory cytokine levels and improved survival after sepsis. These data support not only the contribution of Bid to sepsis-induced apoptosis and the onset of septic morbidity/mortality, but also the existence of a bridge between extrinsic apoptotic signals, e.g., FasL:Fas, TNF:TNFR, and so on, and the intrinsic mitochondrial pathway via Bid-tBid activation during sepsis.

  19. Survival prediction from clinico-genomic models--a comparative study.

    Science.gov (United States)

    Bøvelstad, Hege M; Nygård, Ståle; Borgan, Ornulf

    2009-12-13

    Survival prediction from high-dimensional genomic data is an active field in today's medical research. Most of the proposed prediction methods make use of genomic data alone without considering established clinical covariates that often are available and known to have predictive value. Recent studies suggest that combining clinical and genomic information may improve predictions, but there is a lack of systematic studies on the topic. Also, for the widely used Cox regression model, it is not obvious how to handle such combined models. We propose a way to combine classical clinical covariates with genomic data in a clinico-genomic prediction model based on the Cox regression model. The prediction model is obtained by a simultaneous use of both types of covariates, but applying dimension reduction only to the high-dimensional genomic variables. We describe how this can be done for seven well-known prediction methods: variable selection, unsupervised and supervised principal components regression and partial least squares regression, ridge regression, and the lasso. We further perform a systematic comparison of the performance of prediction models using clinical covariates only, genomic data only, or a combination of the two. The comparison is done using three survival data sets containing both clinical information and microarray gene expression data. Matlab code for the clinico-genomic prediction methods is available at http://www.med.uio.no/imb/stat/bmms/software/clinico-genomic/. Based on our three data sets, the comparison shows that established clinical covariates will often lead to better predictions than what can be obtained from genomic data alone. In the cases where the genomic models are better than the clinical, ridge regression is used for dimension reduction. We also find that the clinico-genomic models tend to outperform the models based on only genomic data. Further, clinico-genomic models and the use of ridge regression gives for all three data sets

  20. The effect of using citric or acetic acid on survival of Listeria monocytogenes during fish protein recovery by isoelectric solubilization and precipitation process.

    Science.gov (United States)

    Otto, R A; Beamer, S; Jaczynski, J; Matak, K E

    2011-10-01

    Isoelectric solubilization and precipitation (ISP) is a protein recovery process effective at reducing Listeria innocua, a nonpathogenic bacterium typically used as a surrogate for L. monocytogenes in recovered trout protein. The response of L. monocytogenes to ISP processing was determined and compared to the response of L. innocua. Headed and gutted rainbow trout were inoculated with L. monocytogenes (10.16 log CFU/g), homogenized, and pH-adjusted with granular citric acid (pH 2.0 and 2.5) or glacial acetic acid (pH 3.0 and 3.5). Proteins were solubilized and centrifugation was used to remove insoluble components (skin, insoluble protein, so on). The supernatant was returned to the protein isoelectric point (pH 5.5) with NaOH and centrifuged to remove precipitated protein. Microbial load was enumerated on both growth and selective media; recovery was not significantly different (P > 0.05). Surviving cells from each component (protein, insoluble, and water) were compared to initial inoculum numbers. Significant reductions were detected at all pH (P acid, with a mean log reduction of 3.03 in the combined components, and a 3.53 log reduction in the protein portion. Data were compared to results from a previous study using L. innocua. Significant differences (P acid type. These results demonstrate the variability in resistance between species and indicate that L. innocua is not an appropriate surrogate for L. monocytogenes for ISP processing with organic acids. © 2011 Institute of Food Technologists®

  1. Reg-2, a downstream signaling protein in the ciliary neurotrophic factor survival pathway, alleviates experimental autoimmune encephalomyelitis

    Directory of Open Access Journals (Sweden)

    Hong eJiang

    2016-05-01

    Full Text Available Ciliary neurotrophic factor (CNTF, originally described as a neurocytokine that could support the survival of neurons, has been recently found to alleviate demyelination, prevent axon loss, and improve functional recovery in a rat model of acute experimental autoimmune encephalomyelitis (EAE. However, poor penetration into the brain parenchyma and unfavorable side effects limit the utility of CNTF. Here, we evaluated the therapeutic potential of a protein downstream of CNTF, regeneration gene protein 2 (Reg-2. Using multiple morphological, molecular biology, and electrophysiological methods to assess neuroinflammation, axonal loss, demyelination, and functional impairment, we observed that Reg-2 and CNTF exert similar effects in the acute phase of EAE. Both treatments attenuated axonal loss and demyelination, improved neuronal survival, and produced functional improvement. With a smaller molecular weight and improved penetration into the brain parenchyma, Reg-2 may be a useful substitute for CNTF therapy in EAE and multiple sclerosis.

  2. Geno3D: automatic comparative molecular modelling of protein.

    Science.gov (United States)

    Combet, Christophe; Jambon, Martin; Deléage, Gilbert; Geourjon, Christophe

    2002-01-01

    Geno3D (http://geno3d-pbil.ibcp.fr) is an automatic web server for protein molecular modelling. Starting with a query protein sequence, the server performs the homology modelling in six successive steps: (i) identify homologous proteins with known 3D structures by using PSI-BLAST; (ii) provide the user all potential templates through a very convenient user interface for target selection; (iii) perform the alignment of both query and subject sequences; (iv) extract geometrical restraints (dihedral angles and distances) for corresponding atoms between the query and the template; (v) perform the 3D construction of the protein by using a distance geometry approach and (vi) finally send the results by e-mail to the user.

  3. Comparative reproductive biology of sympatric species: Nest and chick survival of American avocets and black-necked stilts

    Science.gov (United States)

    Ackerman, Joshua T.; Herzog, Mark P.; Takekawa, John Y.; Hartman, Christopher A.

    2014-01-01

    Identifying differences in reproductive success rates of closely related and sympatrically breeding species can be useful for understanding limitations to population growth. We simultaneously examined the reproductive ecology of American avocets Recurvirostra americana and black-necked stilts Himantopus mexicanus using 1274 monitored nests and 240 radio-marked chicks in San Francisco Bay, California. Although there were 1.8 times more avocet nests than stilt nests, stilts nonetheless fledged 3.3 times more chicks. Greater production by stilts than avocets was the result of greater chick survival from hatching to fledging (avocet: 6%; stilt: 40%), and not because of differences in clutch size (avocet: 3.84; stilt: 3.77), nest survival (avocet: 44%; stilt: 35%), or egg hatching success (avocet: 90%; stilt: 92%). We reviewed the literature and confirmed that nest survival and hatching success are generally similar when avocets and stilts breed sympatrically. In addition to species, chick survival was strongly influenced by age, site, and year. In particular, daily survival rates increased rapidly with chick age, with 70% of mortalities occurring ≤ 1 week after hatch. California gulls Larus californicus caused 55% of avocet, but only 15% of stilt, chick deaths. Differential use of micro-habitats likely reduced stilt chick’s vulnerability to gull predation, particularly during the first week after hatch, because stilts nested in vegetation 2.7 times more often than avocets and vegetation height was 65% taller at stilt nests compared with avocet nests. Our results demonstrate that two co-occurring and closely related species with similar life history strategies can differ markedly in reproductive success, and simultaneous studies of such species can identify differences that limit productivity.

  4. CHD1L Protein is overexpressed in human ovarian carcinomas and is a novel predictive biomarker for patients survival

    Directory of Open Access Journals (Sweden)

    He Wei-Peng

    2012-09-01

    Full Text Available Abstract Background Our recent studies suggested that the chromodomain helicase DNA binding protein 1-like (CHD1L gene plays an oncogenic role in human hepatocellular carcinoma. However, the status of CHD1L protein expression in ovarian cancer and its clinical/prognostic significance are obscure. Methods In this study, immunohistochemistry (IHC for CHD1L was performed on a tissue microarray (TMA containing 102 primary ovarian carcinomas and 44 metastatic lesions (omental metastasis. Receiver-operator curve (ROC analysis was used to evaluate patients’ survival status. Results There is an augmented tendency of CHD1L expression in ovarian carcinoma metastasis than in primary lesions (PP PP Conclusions These findings provide evidence that positive expression of CHD1L protein is significantly correlated with the metastasis proceeding of ovarian carcinoma, and CHD1L protein expression, as examined by IHC, may act as a novel prognostic biomarker for patients with ovarian carcinoma.

  5. Comparing Survival between peritoneal dialysis and hemodialysis patients with subclinical peripheral artery disease: a 6-year follow-up.

    Science.gov (United States)

    Liu, Jiung-Hsiun; Chen, Jan-Yow; Lin, Shih-Yi; Lin, Hsin-Hung; Ting, I-Wen; Liang, Chih-Chia; Wang, I-Kuan; Kuo, Huey-Liang; Chang, Chiz-Tzung; Huang, Chiu-Ching; Sung, Fung-Chang

    2013-01-01

    Peripheral artery disease (PAD) is known to be an increased mortality risk in patients with end-stage renal disease (ESRD). The aim of this study was to compare patient survival between patients with subclinical PAD undergoing peritoneal dialysis (PD) and hemodialysis (HD). Subclinical peripheral artery was defined as an ankle-brachial index of less than 0.9. This study was conducted from April 2005, and the observation period ended on 30 June 2011. At the end of the follow-up, the status of all patients was assessed and data on mortality were obtained for the entire cohort. A total of 91 patients (61 HD and 30 PD) were included for analyses in this study. Mortality rate was 60.0% (18/30) for PD and 52.5% (32/61) for HD. Kaplan-Meier estimate demonstrate that PD patients had a higher mortality rate than those underwent HD (log-rank p = 0.0039). Cox regression model demonstrated that PD was an independent predictor for further mortality in ESRD patients with subclinical peripheral artery disease.(p = 0.012, HR: 1.776, 95% CI: 1.136-2.775). In multivariate analysis, the HD group still had a greater survival than PD group (p = 0.005, HR:1.916, 95% CI: 1.218-3.015). In patients with subclinical peripheral artery disease, the patient survival is better in HD patients as compared with PD patients.

  6. Up-regulation of cell cycle arrest protein BTG2 correlates with increased overall survival in breast cancer, as detected by immunohistochemistry using tissue microarray

    Directory of Open Access Journals (Sweden)

    Jirström Karin

    2010-06-01

    Full Text Available Abstract Background Previous studies have shown that the ADIPOR1, ADORA1, BTG2 and CD46 genes differ significantly between long-term survivors of breast cancer and deceased patients, both in levels of gene expression and DNA copy numbers. The aim of this study was to characterize the expression of the corresponding proteins in breast carcinoma and to determine their correlation with clinical outcome. Methods Protein expression was evaluated using immunohistochemistry in an independent breast cancer cohort of 144 samples represented on tissue microarrays. Fisher's exact test was used to analyze the differences in protein expression between dead and alive patients. We used Cox-regression multivariate analysis to assess whether the new markers predict the survival status of the patients better than the currently used markers. Results BTG2 expression was demonstrated in a significantly lower proportion of samples from dead patients compared to alive patients, both in overall expression (P = 0.026 and cell membrane specific expression (P = 0.013, whereas neither ADIPOR1, ADORA1 nor CD46 showed differential expression in the two survival groups. Furthermore, a multivariate analysis showed that a model containing BTG2 expression in combination with HER2 and Ki67 expression along with patient age performed better than a model containing the currently used prognostic markers (tumour size, nodal status, HER2 expression, hormone receptor status, histological grade, and patient age. Interestingly, BTG2 has previously been described as a tumour suppressor gene involved in cell cycle arrest and p53 signalling. Conclusions We conclude that high-level BTG2 protein expression correlates with prolonged survival in patients with breast carcinoma.

  7. Bee bread increases honeybee haemolymph protein and promote better survival despite of causing higher Nosema ceranae abundance in honeybees.

    Science.gov (United States)

    Basualdo, Marina; Barragán, Sergio; Antúnez, Karina

    2014-08-01

    Adequate protein nutrition supports healthy honeybees and reduces the susceptibility to disease. However little is known concerning the effect of the diet on Nosema ceranae development, an obligate intracellular parasite that disturbs the protein metabolism of honeybees (Apis mellifera). Here we tested the effect of natural (bee bread) and non-natural protein diets (substitute) on haemolymph proteins titers of honeybee and N. ceranae spore production. The natural diet induced higher levels of protein and parasite development, but the survival of bees was also higher than with non-natural diets. The data showed that the administration of an artificially high nutritious diet in terms of crude protein content is not sufficient to promote healthy bees; rather the protein ingested should be efficiently assimilated. The overall results support the idea that the physiological condition of the bees is linked to protein levels in the haemolymph, which affects the tolerance to parasite; consequently the negative impact of the parasite on host fitness is not associated only with the level of infection. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  8. Survival Analysis of Advanced HCC Treated with Radioembolization: Comparing Impact of Clinical Performance Status Versus Vascular Invasion/Metastases.

    Science.gov (United States)

    Ali, Rehan; Gabr, Ahmed; Abouchaleh, Nadine; Al Asadi, Ali; Mora, Ronald A; Kulik, Laura; Abecassis, Michael; Riaz, Ahsun; Salem, Riad; Lewandowski, Robert J

    2017-09-06

    In this study, we aim to compare the effects of prognostic indicators on survival analysis for Barcelona Clinic Liver Cancer (BCLC) C patients undergoing yttrium-90 radioembolization (Y-90). A prospectively acquired database (2003-2017) for BCLC C hepatocellular carcinoma (HCC) patients that underwent radioembolization with Y-90 was searched. The criteria for BCLC C status (Eastern Cooperative Oncology Group (ECOG) performance status (PS) of 1 or 2, metastases, and/or portal vein thrombosis (PVT)) were recorded. Kaplan-Meier survival analyses were performed from the date of the first radioembolization with Y-90, censored to curative treatment, to determine median overall survival (OS). Cox regression hazards model was used for multivariate analyses. Significance was set at P < 0.05. 547 BCLC C patients treated with radioembolization with Y-90 had a median OS of 10.7 months (range: 9.5-12.9). 43% (233 of 547) patients classified as BCLC C solely by their ECOG PS had a median OS of 19.4 months (14.7-23.7); 57% (314 of 547) patients with PVT/metastases had a median OS of 7.7 months (6.7-8.7). On multivariate analysis, ECOG PS was not found to be a statistically significant prognostic indicator of OS in BCLC C whereas metastases and PVT exhibited hazards ratios (95%CI) of 0.51 (0.38-0.69) and 0.49 (0.38-0.63), respectively (P < 0.0001). Patients classified as BCLC C due to ECOG PS 1 demonstrated longer survival when compared to those presenting with PVT, metastases and/or ECOG PS 2. Hence, ECOG PS 1, as an isolated variable, may not be a true indicator of advanced disease.

  9. Major E. coli heat-stress protein do not translocate: implications for cell survival.

    Science.gov (United States)

    Yatvin, M B; Clark, A W; Siegel, F L

    1987-10-01

    When Escherichia coli are exposed to heat stress, the majority of proteins in the process of synthesis at the time of heat stress are rapidly translocated to the outer membrane of the bacterium. The synthesis of most of these proteins appears to take place on membrane-bound polyribosomes. With the temperature shift, overall protein synthesis is inhibited while the synthesis of a small group of proteins is initiated. These proteins are not translocated, but remain in the cytosolic compartment, and they are identifiable as heat-stress proteins. Both the translocation phenomenon and the retention of heat-stress proteins in the cytosolic compartment in proximity to the nucleoid could counteract the effects of heat stress. The translocated proteins may operate by stabilizing the outer membrane prior to the induction of heat-stress proteins and the latter, which are confined to the cytoplasmic compartment, may serve to protect the integrity of the nucleoid structures.

  10. A novel method to compare protein structures using local descriptors

    Directory of Open Access Journals (Sweden)

    Daniluk Paweł

    2011-08-01

    Full Text Available Abstract Background Protein structure comparison is one of the most widely performed tasks in bioinformatics. However, currently used methods have problems with the so-called "difficult similarities", including considerable shifts and distortions of structure, sequential swaps and circular permutations. There is a demand for efficient and automated systems capable of overcoming these difficulties, which may lead to the discovery of previously unknown structural relationships. Results We present a novel method for protein structure comparison based on the formalism of local descriptors of protein structure - DEscriptor Defined Alignment (DEDAL. Local similarities identified by pairs of similar descriptors are extended into global structural alignments. We demonstrate the method's capability by aligning structures in difficult benchmark sets: curated alignments in the SISYPHUS database, as well as SISY and RIPC sets, including non-sequential and non-rigid-body alignments. On the most difficult RIPC set of sequence alignment pairs the method achieves an accuracy of 77% (the second best method tested achieves 60% accuracy. Conclusions DEDAL is fast enough to be used in whole proteome applications, and by lowering the threshold of detectable structure similarity it may shed additional light on molecular evolution processes. It is well suited to improving automatic classification of structure domains, helping analyze protein fold space, or to improving protein classification schemes. DEDAL is available online at http://bioexploratorium.pl/EP/DEDAL.

  11. Analysis of conglutin seed storage proteins across lupin species using transcriptomic, protein and comparative genomic approaches.

    Science.gov (United States)

    Foley, Rhonda C; Jimenez-Lopez, Jose C; Kamphuis, Lars G; Hane, James K; Melser, Su; Singh, Karam B

    2015-04-19

    The major proteins in lupin seeds are conglutins that have primary roles in supplying carbon, sulphur and nitrogen and energy for the germinating seedling. They fall into four families; α, β, γ and δ. Interest in these conglutins is growing as family members have been shown to have beneficial nutritional and pharmaceutical properties. An in-depth transcriptome and draft genome from the narrow-leafed lupin (NLL; Lupinus angustifolius) variety, Tanjil, were examined and 16 conglutin genes were identified. Using RNAseq data sets, the structure and expression of these 16 conglutin genes were analysed across eight lupin varieties from five lupin species. Phylogenic analysis suggest that the α and γ conglutins diverged prior to lupin speciation while β and δ members diverged both prior and after speciation. A comparison of the expression of the 16 conglutin genes was performed, and in general the conglutin genes showed similar levels of RNA expression among varieties within species, but quite distinct expression patterns between lupin species. Antibodies were generated against the specific conglutin families and immunoblot analyses were used to compare the levels of conglutin proteins in various tissues and during different stages of seed development in NLL, Tanjil, confirming the expression in the seed. This analysis showed that the conglutins were expressed highly at the mature seed stage, in all lupin species, and a range of polypeptide sizes were observed for each conglutin family. This study has provided substantial information on the complexity of the four conglutin families in a range of lupin species in terms of their gene structure, phylogenetic relationships as well as their relative RNA and protein abundance during seed development. The results demonstrate that the majority of the heterogeneity of conglutin polypeptides is likely to arise from post-translational modification from a limited number of precursor polypeptides rather than a large number of

  12. Comparative analysis of vitamin C, crude protein, elemental nitrogen ...

    African Journals Online (AJOL)

    This study aims at promoting the consumption of canola greens (Brassica napus L.) as alternative, affordable and available dietary sources of vitamin C, minerals and protein. As one of the oldest-known forms in cabbages family, kale (Brassica oleracea var. acephala L.) greens are among the most consumed vegetable ...

  13. Toxoplasma gondii autophagy-related protein ATG9 is crucial for the survival of parasites in their host.

    Science.gov (United States)

    Nguyen, Hoa Mai; El Hajj, Hiba; El Hajj, Rana; Tawil, Nadim; Berry, Laurence; Lebrun, Maryse; Bordat, Yann; Besteiro, Sébastien

    2017-06-01

    Autophagy is a conserved, life-promoting, catabolic process involved in the recycling of nonessential cellular components in response to stress. The parasite Toxoplasma gondii is an early-diverging eukaryote in which part of the autophagy machinery is not exclusively involved in a catabolic process but instead has been repurposed for an original function in organelle inheritance during cell division. This function, depending essentially on protein TgATG8 and its membrane conjugation system, is crucial for parasite survival and prevented an in depth study of autophagy in the mutants generated so far in Toxoplasma. Thus, in order to decipher the primary function of canonical autophagy in the parasites, we generated a cell line deficient for TgATG9, a protein thought to be involved in the early steps of the autophagy process. Although the protein proved to be dispensable for the development of these obligate intracellular parasites in vitro, the absence of TgATG9 led to a reduced ability to sustain prolonged extracellular stress. Importantly, depletion of the protein significantly reduced parasites survival in macrophages and markedly attenuated their virulence in mice. Altogether, this shows TgATG9 is important for the fate of Toxoplasma in immune cells and contributes to the overall virulence of the parasite, possibly through an involvement in a canonical autophagy pathway. © 2016 John Wiley & Sons Ltd.

  14. Providing supplemental milk to piglets preweaning improves the growth but not survival of gilt progeny compared with sow progeny.

    Science.gov (United States)

    Miller, Y J; Collins, A M; Smits, R J; Thomson, P C; Holyoake, P K

    2012-12-01

    Gilt progeny have lighter weaning weights and greater postweaning medication and mortality rates compared with the progeny of older parity sows. Because weaning weight has been positively correlated with postweaning survival, this study aimed to determine whether the provision of supplemental milk preweaning could improve weaning weight and subsequent weights as well as postweaning survival of gilt progeny. The study was replicated in summer and winter as the effects of supplemental milk were expected to vary with season. The progeny of 80 gilts (parity 0) and 80 sows (parity 2 to 5) were allocated to both treatments: with or without supplemental milk in these 2 seasons with 5 sheds/season. Litter size was standardized (10 to 11 piglets) and each piglet was weighed at birth, d 21, weaning (4 wk), and 10 wk of age. Medications and mortalities were recorded both preweaning and postweaning. Pigs were housed within treatment groups postweaning, and ADFI and G:F were measured. Gilt progeny were 200 g lighter at birth in both replicates (P gilt and sow progeny by 800 g in summer (P gilts or sows (P > 0.05). Supplemental milk disappearance (the daily difference between the volume of milk provided and the residue left in the drinker) was greater in summer than winter (by 130 mL/piglet d(-1); P gilt progeny reached or exceeded that of nonsupplemented sow progeny. Gilt progeny had greater postweaning mortality (2.6%) and medication rates (6.2%) than sow progeny (1 and 2.2%, respectively; both P Gilt progeny also had less postweaning ADFI than sow progeny in winter (528 and 636 g, respectively; P 0.05). The hypothesis that supplemental milk provision did increase gilt progeny weaning weight was supported (especially in summer) but the supplementation had no effect on postweaning weights and survival. Efforts to improve gilt progeny postweaning growth and survival need to be aimed at improving health and immunity, not just weaning weight.

  15. Resin Versus Glass Microspheres for90Y Transarterial Radioembolization: Comparing Survival in Unresectable Hepatocellular Carcinoma Using Pretreatment Partition Model Dosimetry.

    Science.gov (United States)

    Van Der Gucht, Axel; Jreige, Mario; Denys, Alban; Blanc-Durand, Paul; Boubaker, Ariane; Pomoni, Anastasia; Mitsakis, Periklis; Silva-Monteiro, Marina; Gnesin, Silvano; Lalonde, Marie Nicod; Duran, Rafael; Prior, John O; Schaefer, Niklaus

    2017-08-01

    The aim of this study was to compare survival of patients treated for unresectable hepatocellular carcinoma (uHCC) with 90 Y transarterial radioembolization (TARE) using pretreatment partition model dosimetry (PMD). Methods: We performed a retrospective analysis of prospectively collected data on 77 patients consecutively treated (mean age ± SD, 66.4 ± 12.2 y) for uHCC (36 uninodular, 5 multinodular, 36 diffuse) with 90 Y TARE (41 resin, 36 glass) using pretreatment PMD. Study endpoints were progression-free survival (PFS) and overall survival (OS) assessed by Kaplan-Meier estimates. Several variables including Barcelona Clinic Liver Cancer (BCLC) staging system, tumor size, and serum α-fetoprotein (AFP) level were investigated using Cox proportional hazards regression. Results: The characteristics of 2 groups were comparable with regard to demographic data, comorbidities, Child-Pugh score, BCLC, serum AFP level, and 90 Y global administered activity. The median follow-up time was 7.7 mo (range, 0.4-50.1 mo). Relapse occurred in 44 patients (57%) at a median of 6 mo (range, 0.4-27.9 mo) after 90 Y TARE, and 41 patients (53%) died from tumor progression. Comparison between resin and glass microspheres revealed higher but not statistically significantly PFS and OS rates in the 90 Y resin group than the 90 Y glass group (resin PFS 6.1 mo [95% confidence interval CI, 4.7-7.4] and glass PFS 5 mo [95% CI, 0.9-9.2], P = 0.53; resin OS 7.7 mo [95% CI, 7.2-8.2] and glass OS 7 mo [95% CI 1.6-12.4], P = 0.77). No significant survival difference between both types of 90 Y microspheres was observed in any subgroups of patients with early/intermediate or advanced BCLC stages. Among the variables investigated, Cox analyses showed that only in the glass group, the BCLC staging system and the serum AFP level were associated with PFS ( P = 0.04) and OS ( P = 0.04). Tumor size was a prognostic factor without significant influence on PFS and OS after 90 Y TARE. Conclusion

  16. Comparative Analysis of Clinical, Treatment, and Survival Characteristics of Basaloid and Squamous Cell Carcinoma of the Esophagus.

    Science.gov (United States)

    Salami, Aitua; Abbas, Abbas E; Petrov, Roman; Jhala, Nirag; Bakhos, Charles T

    2017-11-11

    Basaloid squamous cell carcinoma (BSC) is a rare variant of squamous cell carcinoma (SqCC) of the esophagus. Even though pathologically thought to be more aggressive than SqCC, there is discrepancy in the literature regarding the outcomes of BSC compared with those of SqCC. We conducted a retrospective cohort study using the Surveillance Epidemiology and End Results (SEER) database. All patients with a histologic diagnosis of BSC and SqCC between 2004 and 2013 were included. We compared treatment and survival characteristics of patients with BSC and SqCC. There were 16,158 patients included in this study; 173 patients (1.1%) had BSC. There were no significant differences between the 2 groups based on age, sex, marital status, insurance, or geographic region of diagnosis, but patients with BSC were more likely to be Caucasian (73.4% vs 64.7%; p = 0.017). Among staged patients, baseline tumor stage was similar in both groups. However, BSC tumors were more likely to be of high pathologic grade (56.8% vs 38.2%; p BSC were more likely to undergo resection (32.4% vs 17.0%; p BSC of the esophagus seems to have similar clinical features and survival outcomes when compared with SqCC. Patients with BSC and SqCC should undergo stage-specific treatment to achieve optimal outcomes. Copyright © 2017 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

  17. Concurrent alterations of RAGE, RECK, and MMP9 protein expression are relevant to Epstein-Barr virus infection, metastasis, and survival in nasopharyngeal carcinoma.

    Science.gov (United States)

    Zhou, Dong-Ni; Deng, Yan-Fei; Li, Rong-Hua; Yin, Ping; Ye, Chun-Sheng

    2014-01-01

    This study aimed to concurrently investigate the expressions of receptor for advanced glycation end products (RAGE), reversion inducing cysteine-rich protein with Kazal motifs (RECK) and matrix metalloproteinase 9 (MMP9) in nasopharyngeal carcinoma (NPC) and their correlations with clinicopathological properties. Using immunohistochemistry, we found that RECK expression was downregulated in NPC tissues compared with chronic nasopharyngitis (CNT) tissues, while RAGE and MMP9 expressions were upregulated. We further found that RECK expression level was inversely correlated with MMP9 expression level in NPC, whereas RAGE expression level was positively correlated with MMP9 expression level. Moreover, aberrant expressions of these proteins had a positive correlation with the titers of EBVCA-IgA, lymphatic metastasis, recurrence and survival. Together, these findings suggest that dysregulations of RECK and RAGE expressions may be collectively involved in tumor progression of NPC by regulating MMP9 expression and that they may be a good prognostic predictors for NPC.

  18. Small grain cereals compared for dietary fibre and protein contents

    Directory of Open Access Journals (Sweden)

    Žilić Slađana

    2011-01-01

    Full Text Available The content of dietary fibres (cellulose, hemicellulose, lignin, NDF, ADF, tryptophan and proteins, as well as their quality index were determined in whole grains of bread and durum wheat, rye, hull-less barley and hull-less oat, each represented with four genotypes. In addition, content of β-glucans in hull-less barley were determined. In average, hull-less barley and oat had the lowest content of hemicellulose (22.54 and 13.11% d.m., respectively, cellulose (1.36 and 1.41% d.m., respectively, lignin (0.98 and 0.49% d.m., respectively, as well as NDF (24.84 and 15.16% d.m., respectively and ADF (2.30 and 2.04% d.m., respectively. In average, the highest content of hemicellulose was in durum wheat (33.47% d.m., followed by rye (29.63% d.m., and bread wheat (23.24% d.m.. Among tested hull-less barley genotypes the the content of β-glucans ranged from 4.1% d.m. (IWHBON 97-18 to 5.6% d.m. (Apolon. The highest content of proteins (on average 15.65% d.m. and tryptophan (on average 0.206% d.m. was in hull-less oat. Hull-less barley had the highest protein quality index (1.48% followed by bread and durum wheat and hull-less oat (IQ 1.35, 1.34 and 1.31%, respectively, and rye (IQ 0.93%. The results indicate that there is genetic diversity in content of dietary fibres and proteins among tested genotypes and that it should be possible to selectively breed for lines with high nutrition capacities, as well as, to improved diet requirements.

  19. Loss of BRCA1 protein expression as indicator of the BRCAness phenotype is associated with favorable overall survival after complete resection of sporadic ovarian cancer.

    Science.gov (United States)

    Radosa, Marc P; Häfner, Norman; Camara, Oumar; Diebolder, Herbert; Mothes, Anke; Winzer, Harald; Jansen, Lars; Dürst, Matthias; Runnebaum, Ingo B

    2011-11-01

    Hereditary epithelial ovarian cancers (EOCs) not expressing functional BRCA1 protein are characterized by defects in homologous recombination DNA repair, rendering such tumors more sensitive to DNA damaging agents and synthetic lethality, that is, poly-ADP-ribose-polymerase inhibitor treatment. The aim of this study was to evaluate the use of BRCA1 immunohistochemistry (IHC) for EOC prognosis and identification of features of the BRCAness phenotype. Twenty-seven patients who were treated for advanced EOC by macroscopic complete surgical tumor resection and first-line carboplatin/paclitaxel treatment were included. Time to recurrence and overall survival time after initial surgery were determined, and patients' samples were evaluated for BRCA1 expression by IHC. BRCA1 messenger RNA expression and promoter methylation was analyzed to elucidate regulatory mechanisms involved in BRCA1 protein loss. BRCA1 IHC-negative patients had a significantly longer overall survival (crude rate, 1537 days) compared to the BRCA1 IHC-positive group (crude rate, 827 days; P = 0.01). The patients in the BRCA1 IHC-negative group were significantly younger (51 years) compared to BRCA1 IHC-positive patients (61 years; P IHC negativity of sporadic EOC may be predictive of sensitivity to platinum-based chemotherapy and the poly-ADP-ribose-polymerase inhibitor-sensitive BRCAness phenotype.

  20. Comparing the effects of endogenous and synthetic cannabinoid receptor agonists on survival of gastric cancer cells.

    Science.gov (United States)

    Ortega, A; García-Hernández, V M; Ruiz-García, E; Meneses-García, A; Herrera-Gómez, A; Aguilar-Ponce, J L; Montes-Servín, E; Prospero-García, O; Del Angel, S A

    2016-11-15

    Anti-neoplastic activity induced by cannabinoids has been extensively documented for a number of cancer cell types; however, this topic has been explored in gastric cancer cells only in a limited number of approaches. Thus, the need of integrative and comparative studies still persists. In this study we tested and compared the effects of three different cannabinoid receptor agonists-anandamide (AEA), (R)-(+)-methanandamide (Meth-AEA) and CP 55,940 (CP)- on gastric cancer cell morphology, viability and death events in order to provide new insights to the use of these agents for therapeutic purposes. The three agents tested exhibited similar concentration-dependent effects in the induction of changes in cell morphology and cell loss, as well as in the decrease of cell viability and DNA laddering in the human gastric adenocarcinoma cell line (AGS). Differences among the cannabinoids tested were mostly observed in the density of cells found in early and late apoptosis and necrosis, favoring AEA and CP as the more effective inducers of apoptotic mechanisms, and Meth-AEA as a more effective inducer of necrosis through transient and rapid apoptosis. Through a comparative approach, our results support and confirm the therapeutic potential that cannabinoid receptor agonists exert in gastric cancer cells and open possibilities to use cannabinoids as part of a new gastric cancer therapy. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Inhibition of the leucine-rich repeat protein LINGO-1 enhances survival, structure, and function of dopaminergic neurons in Parkinson's disease models.

    Science.gov (United States)

    Inoue, Haruhisa; Lin, Ling; Lee, Xinhua; Shao, Zhaohui; Mendes, Shannon; Snodgrass-Belt, Pamela; Sweigard, Harry; Engber, Tom; Pepinsky, Blake; Yang, Lichuan; Beal, M Flint; Mi, Sha; Isacson, Ole

    2007-09-04

    The nervous system-specific leucine-rich repeat Ig-containing protein LINGO-1 is associated with the Nogo-66 receptor complex and is endowed with a canonical EGF receptor (EGFR)-like tyrosine phosphorylation site. Our studies indicate that LINGO-1 expression is elevated in the substantia nigra of Parkinson's disease (PD) patients compared with age-matched controls and in animal models of PD after neurotoxic lesions. LINGO-1 expression is present in midbrain dopaminergic (DA) neurons in the human and rodent brain. Therefore, the role of LINGO-1 in cell damage responses of DA neurons was examined in vitro and in experimental models of PD induced by either oxidative (6-hydroxydopamine) or mitochondrial (N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) toxicity. In LINGO-1 knockout mice, DA neuron survival was increased and behavioral abnormalities were reduced compared with WT. This neuroprotection was accompanied by increased Akt phosphorylation (p-Akt). Similar neuroprotective in vivo effects on midbrain DA neurons were obtained in WT mice by blocking LINGO-1 activity using LINGO-1-Fc protein. Neuroprotection and enhanced neurite growth were also demonstrated for midbrain DA neurons in vitro. LINGO-1 antagonists (LINGO-1-Fc, dominant negative LINGO-1, and anti-LINGO-1 antibody) improved DA neuron survival in response to MPP+ in part by mechanisms that involve activation of the EGFR/Akt signaling pathway through a direct inhibition of LINGO-1's binding to EGFR. These results show that inhibitory agents of LINGO-1 activity can protect DA neurons against degeneration and indicate a role for the leucine-rich repeat protein LINGO-1 and related classes of proteins in the pathophysiological responses of midbrain DA neurons in PD.

  2. Urokinase mediates endothelial cell survival via induction of the X-linked inhibitor of apoptosis protein

    DEFF Research Database (Denmark)

    Prager, Gerald W; Mihaly, Judit; Brunner, Patrick M

    2008-01-01

    ), but independent of the phosphatidylinositol 3 (PI3) kinase pathway, whereas vascular endothelial growth factor (VEGF)-induced antiapoptosis was PI3 kinase dependent. uPA-induced cell survival involved phosphorylation of p21-activated kinase 1 (Pak1) and the IkappaB kinase alpha that leads to nuclear factor kappa...

  3. Survival of motor neuron protein downregulates miR-9 expression in patients with spinal muscular atrophy

    Directory of Open Access Journals (Sweden)

    Li-Ting Wang

    2014-05-01

    Full Text Available Spinal muscular atrophy (SMA is a lethal hereditary disease caused by homozygous absence of the survival of the motor neuron (SMN 1 gene (SMN1, and it is the leading genetic cause of infant mortality. The severity of SMA is directly correlated with SMN protein levels in affected patients; however, the cellular regulatory mechanisms for SMN protein expression are not completely understood. In this study, we investigated the regulatory effects between SMN expression and miR-9a, a downstream noncoding small RNA. Using an inducible SMN short hairpin RNA interference (shRNAi system in NSC 34 and human skin fibroblast cells, cellular miR-9 levels and SMN protein repression were time-dependently upregulated. Conversely, cellular miR-9 levels decreased when HeLa cells were transfected with SMN protein fused with green fluorescent protein. In SMA-like mice spinal cords and human primary skin fibroblasts isolated from patients with different degrees of SMA, human SMN exhibited a disease severity-dependent decrease, whereas cellular miR-9 levels increased. These results clearly suggested that cellular SMN proteins regulated miR-9 expression and that miR-9 expression was related to SMA severity. Thus, miR-9 may be a marker for SMA prognosis.

  4. CPEB4 is a cell survival protein retained in the nucleus upon ischemia or endoplasmic reticulum calcium depletion.

    Science.gov (United States)

    Kan, Ming-Chung; Oruganty-Das, Aparna; Cooper-Morgan, Amalene; Jin, Guang; Swanger, Sharon A; Bassell, Gary J; Florman, Harvey; van Leyen, Klaus; Richter, Joel D

    2010-12-01

    The RNA binding protein CPEB (cytoplasmic polyadenylation element binding) regulates cytoplasmic polyadenylation and translation in germ cells and the brain. In neurons, CPEB is detected at postsynaptic sites, as well as in the cell body. The related CPEB3 protein also regulates translation in neurons, albeit probably not through polyadenylation; it, as well as CPEB4, is present in dendrites and the cell body. Here, we show that treatment of neurons with ionotropic glutamate receptor agonists causes CPEB4 to accumulate in the nucleus. All CPEB proteins are nucleus-cytoplasm shuttling proteins that are retained in the nucleus in response to calcium-mediated signaling and alpha-calcium/calmodulin-dependent kinase protein II (CaMKII) activity. CPEB2, -3, and -4 have conserved nuclear export signals that are not present in CPEB. CPEB4 is necessary for cell survival and becomes nuclear in response to focal ischemia in vivo and when cultured neurons are deprived of oxygen and glucose. Further analysis indicates that nuclear accumulation of CPEB4 is controlled by the depletion of calcium from the ER, specifically, through the inositol-1,4,5-triphosphate (IP3) receptor, indicating a communication between these organelles in redistributing proteins between subcellular compartments.

  5. CPEB4 Is a Cell Survival Protein Retained in the Nucleus upon Ischemia or Endoplasmic Reticulum Calcium Depletion ▿ †

    Science.gov (United States)

    Kan, Ming-Chung; Oruganty-Das, Aparna; Cooper-Morgan, Amalene; Jin, Guang; Swanger, Sharon A.; Bassell, Gary J.; Florman, Harvey; van Leyen, Klaus; Richter, Joel D.

    2010-01-01

    The RNA binding protein CPEB (cytoplasmic polyadenylation element binding) regulates cytoplasmic polyadenylation and translation in germ cells and the brain. In neurons, CPEB is detected at postsynaptic sites, as well as in the cell body. The related CPEB3 protein also regulates translation in neurons, albeit probably not through polyadenylation; it, as well as CPEB4, is present in dendrites and the cell body. Here, we show that treatment of neurons with ionotropic glutamate receptor agonists causes CPEB4 to accumulate in the nucleus. All CPEB proteins are nucleus-cytoplasm shuttling proteins that are retained in the nucleus in response to calcium-mediated signaling and alpha-calcium/calmodulin-dependent kinase protein II (CaMKII) activity. CPEB2, -3, and -4 have conserved nuclear export signals that are not present in CPEB. CPEB4 is necessary for cell survival and becomes nuclear in response to focal ischemia in vivo and when cultured neurons are deprived of oxygen and glucose. Further analysis indicates that nuclear accumulation of CPEB4 is controlled by the depletion of calcium from the ER, specifically, through the inositol-1,4,5-triphosphate (IP3) receptor, indicating a communication between these organelles in redistributing proteins between subcellular compartments. PMID:20937770

  6. Methylation and protein expression of DNA repair genes: association with chemotherapy exposure and survival in sporadic ovarian and peritoneal carcinomas

    Directory of Open Access Journals (Sweden)

    Walsh Tom

    2009-07-01

    Full Text Available Abstract Background DNA repair genes critically regulate the cellular response to chemotherapy and epigenetic regulation of these genes may be influenced by chemotherapy exposure. Restoration of BRCA1 and BRCA2 mediates resistance to platinum chemotherapy in recurrent BRCA1 and BRCA2 mutated hereditary ovarian carcinomas. We evaluated BRCA1, BRCA2, and MLH1 protein expression in 115 sporadic primary ovarian carcinomas, of which 31 had paired recurrent neoplasms collected after chemotherapy. Additionally, we assessed whether promoter methylation of BRCA1, MLH1 or FANCF influenced response to chemotherapy or explained alterations in protein expression after chemotherapy exposure. Results Of 115 primary sporadic ovarian carcinomas, 39 (34% had low BRCA1 protein and 49 (42% had low BRCA2 expression. BRCA1 and BRCA2 protein expression were highly concordant (p Conclusion Low BRCA1 expression in primary sporadic ovarian carcinoma is associated with prolonged survival. Recurrent ovarian carcinomas commonly have increased BRCA1 and/or BRCA2 protein expression post chemotherapy exposure which could mediate resistance to platinum based therapies. However, alterations in expression of these proteins after chemotherapy are not commonly mediated by promoter methylation, and other regulatory mechanisms are likely to contribute to these alterations.

  7. Comparing environmental issues in Cuba before and after the Special Period: balancing sustainable development and survival.

    Science.gov (United States)

    Maal-Bared, Rasha

    2006-04-01

    Following the Earth Summit in 1992, Cuba designed and implemented a variety of programs, administrative structures, and public awareness activities to promote sound environmental management and sustainable development. This came shortly after the fall of the Soviet Union and the strengthening of the US blockade in 1990, which resulted in a 35% drop in Cuban GDP. This period, referred to as the Special Period, witnessed a decrease in many environmentally damaging activities both by choice and by necessity, but also resulted in many decisions to resuscitate the Cuban economy. The purpose of this work was to compare and rank the environmental risks Cuba faced before and during the Special Period (1990-2000) using two Comparative environmental risk assessments (CERAs). To do so, an ecosystem integrity risk assessment matrix was constructed with 42 risk end points. The matrix assessed the risk posed by 17 problem areas including air pollution, water contamination, solid waste sites, pesticides and ecosystem degradation. The risks were calculated using five criteria: area affected, vulnerability of affected population, severity of impact, irreversibility of effect and uncertainty. To construct this matrix, both literature reviews and expert interviews in Cuba were conducted in 2000. The results showed a general decrease in risk scores during the Special Period. Before the Special Period, high risks were posed by: terrestrial degradation and industrial wastewater and sludge, followed by freshwater degradation, surface water stressors, and pesticides. After the Special Period, industrial wastewater and sludge and pesticides were no longer high-risk areas, but municipal wastewater and marine coastal degradation ranked higher than previously. Also, the risk endpoints most stressed after 1990 were affected by activities controlled by the government, such as mining and tourism, and lack of infrastructure. Therefore, the claims that public environmental education is the main

  8. Comparative transcriptional analysis of Bacillus subtilis cells overproducing either secreted proteins, lipoproteins or membrane proteins

    Directory of Open Access Journals (Sweden)

    Marciniak Bogumiła C

    2012-05-01

    Full Text Available Abstract Background Bacillus subtilis is a favorable host for the production of industrially relevant proteins because of its capacity of secreting proteins into the medium to high levels, its GRAS (Generally Recognized As Safe status, its genetic accessibility and its capacity to grow in large fermentations. However, production of heterologous proteins still faces limitations. Results This study aimed at the identification of bottlenecks in secretory protein production by analyzing the response of B. subtilis at the transcriptome level to overproduction of eight secretory proteins of endogenous and heterologous origin and with different subcellular or extracellular destination: secreted proteins (NprE and XynA of B. subtilis, Usp45 of Lactococcus lactis, TEM-1 β-lactamase of Escherichia coli, membrane proteins (LmrA of L. lactis and XylP of Lactobacillus pentosus and lipoproteins (MntA and YcdH of B. subtilis. Responses specific for proteins with a common localization as well as more general stress responses were observed. The latter include upregulation of genes encoding intracellular stress proteins (groES/EL, CtsR regulated genes. Specific responses include upregulation of the liaIHGFSR operon under Usp45 and TEM-1 β-lactamase overproduction; cssRS, htrA and htrB under all secreted proteins overproduction; sigW and SigW-regulated genes mainly under membrane proteins overproduction; and ykrL (encoding an HtpX homologue specifically under membrane proteins overproduction. Conclusions The results give better insights into B. subtilis responses to protein overproduction stress and provide potential targets for genetic engineering in order to further improve B. subtilis as a protein production host.

  9. Comparative transcriptional analysis of Bacillus subtilis cells overproducing either secreted proteins, lipoproteins or membrane proteins.

    Science.gov (United States)

    Marciniak, Bogumiła C; Trip, Hein; van-der Veek, Patricia J; Kuipers, Oscar P

    2012-05-24

    Bacillus subtilis is a favorable host for the production of industrially relevant proteins because of its capacity of secreting proteins into the medium to high levels, its GRAS (Generally Recognized As Safe) status, its genetic accessibility and its capacity to grow in large fermentations. However, production of heterologous proteins still faces limitations. This study aimed at the identification of bottlenecks in secretory protein production by analyzing the response of B. subtilis at the transcriptome level to overproduction of eight secretory proteins of endogenous and heterologous origin and with different subcellular or extracellular destination: secreted proteins (NprE and XynA of B. subtilis, Usp45 of Lactococcus lactis, TEM-1 β-lactamase of Escherichia coli), membrane proteins (LmrA of L. lactis and XylP of Lactobacillus pentosus) and lipoproteins (MntA and YcdH of B. subtilis). Responses specific for proteins with a common localization as well as more general stress responses were observed. The latter include upregulation of genes encoding intracellular stress proteins (groES/EL, CtsR regulated genes). Specific responses include upregulation of the liaIHGFSR operon under Usp45 and TEM-1 β-lactamase overproduction; cssRS, htrA and htrB under all secreted proteins overproduction; sigW and SigW-regulated genes mainly under membrane proteins overproduction; and ykrL (encoding an HtpX homologue) specifically under membrane proteins overproduction. The results give better insights into B. subtilis responses to protein overproduction stress and provide potential targets for genetic engineering in order to further improve B. subtilis as a protein production host.

  10. Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

    Directory of Open Access Journals (Sweden)

    Boucher Charles AB

    2010-07-01

    Full Text Available Abstract Background The National Institute of Allergy and Infectious Diseases has launched the HIV-1 Human Protein Interaction Database in an effort to catalogue all published interactions between HIV-1 and human proteins. In order to systematically investigate these interactions functionally and dynamically, we have constructed an HIV-1 human protein interaction network. This network was analyzed for important proteins and processes that are specific for the HIV life-cycle. In order to expose viral strategies, network motif analysis was carried out showing reoccurring patterns in virus-host dynamics. Results Our analyses show that human proteins interacting with HIV form a densely connected and central sub-network within the total human protein interaction network. The evaluation of this sub-network for connectivity and centrality resulted in a set of proteins essential for the HIV life-cycle. Remarkably, we were able to associate proteins involved in RNA polymerase II transcription with hubs and proteasome formation with bottlenecks. Inferred network motifs show significant over-representation of positive and negative feedback patterns between virus and host. Strikingly, such patterns have never been reported in combined virus-host systems. Conclusions HIV infection results in a reprioritization of cellular processes reflected by an increase in the relative importance of transcriptional machinery and proteasome formation. We conclude that during the evolution of HIV, some patterns of interaction have been selected for resulting in a system where virus proteins preferably interact with central human proteins for direct control and with proteasomal proteins for indirect control over the cellular processes. Finally, the patterns described by network motifs illustrate how virus and host interact with one another.

  11. Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

    NARCIS (Netherlands)

    van Dijk, D.; Ertaylan, G.; Boucher, C.A.B.; Sloot, P.M.A.

    2010-01-01

    Background: The National Institute of Allergy and Infectious Diseases has launched the HIV-1 Human Protein Interaction Database in an effort to catalogue all published interactions between HIV-1 and human proteins. In order to systematically investigate these interactions functionally and

  12. Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

    NARCIS (Netherlands)

    D. van Dijk (David); G. Ertaylan (Gokhan); C.A.B. Boucher (Charles); P.M.A. Sloot (Peter)

    2010-01-01

    textabstractBackground: The National Institute of Allergy and Infectious Diseases has launched the HIV-1 Human Protein Interaction Database in an effort to catalogue all published interactions between HIV-1 and human proteins. In order to systematically investigate these interactions functionally

  13. A survival analysis comparing women with ovarian low-grade serous carcinoma to those with high-grade histology

    Directory of Open Access Journals (Sweden)

    Chen M

    2014-10-01

    Full Text Available Ming Chen,1 Ying Jin,1 Yalan Bi,2 Jie Yin,1 Yongxue Wang,1 Lingya Pan1 1Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China; 2Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China Abstract: Ovarian low-grade serous carcinoma (LGSC and high-grade serous carcinoma have distinct molecular profiles, clinical behaviors, and treatment responses. The survival advantage for patients with low-grade carcinoma compared with patients with high-grade histology remains controversial. We retrospectively reviewed the medical charts of 381 patients with ovarian serous carcinoma at Peking Union Medical College Hospital from 2007 to 2010. Patients were classified into two groups according to MD Anderson two-tier system: 35 (9.2% cases with LGSC and 346 with high-grade serous carcinoma. Patients with low-grade serous ovarian cancer had a significantly younger age at diagnosis (46 versus 56 years, P=0.046, and their median progression-free survival (PFS and overall survival values were 35.0 and 54.0 months, respectively. A multivariate analysis showed that, for serous ovarian cancer, the histological grade was a significant prognostic factor for PFS but not for overall survival (P=0.022 and P=0.0566, respectively. When stratified by the existence of a residual disease, patients with low-grade disease who underwent cytoreductive surgery without macroscopic residual disease (>1 cm had a significantly improved median PFS time (36.0 months compared with that of patients with high-grade carcinoma who received optimal cytoreductive surgery (16.0 months, P=0.017. Conversely, patients with low-grade and high-grade carcinoma who were left with macroscopic residue (>1 cm experienced a similarly shorter median PFS (10.0 and 13

  14. Comparative evaluation of extraction methods for apoplastic proteins from maize leaves

    Directory of Open Access Journals (Sweden)

    Witzel Katja

    2011-12-01

    Full Text Available Abstract Proteins in the plant apoplast are essential for many physiological processes. We have analysed and compared six different infiltration solutions for proteins contained in the apoplast to recognize the most suitable method for leaves and to establish proteome maps for each extraction. The efficiency of protocols was evaluated by comparing the protein patterns resolved by 1-DE and 2-DE, and revealed distinct characteristics for each infiltration solution. Nano-LC-ESI-Q-TOF MS analysis of all fractions was applied to cover all proteins differentially extracted by infiltration solutions and led to the identification of 328 proteins in total in apoplast preparations. The predicted subcellular protein localisation distinguished the examined infiltration solutions in those with high or low amounts of intracellular protein contaminations, and with high or low quantities of secreted proteins. All tested infiltration solution extracted different subsets of proteins, and those implications on apoplast-specific studies are discussed.

  15. Experimental exposure to cadmium affects metallothionein-like protein levels but not survival and growth in wolf spiders from polluted and reference populations

    Energy Technology Data Exchange (ETDEWEB)

    Eraly, Debbie, E-mail: debbie.eraly@ugent.b [Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent (Belgium); Hendrickx, Frederik, E-mail: frederik.hendrickx@naturalsciences.b [Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent (Belgium); Royal Belgian Institute of Natural Sciences, Department of Entomology, Vautierstraat 29, 1000 Brussels (Belgium); Bervoets, Lieven, E-mail: lieven.bervoets@ua.ac.b [Ecophysiology, Biochemistry and Toxicology Group, Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Lens, Luc, E-mail: luc.lens@ugent.b [Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent (Belgium)

    2010-06-15

    Both local adaptation and acclimation in tolerance mechanisms may allow populations to persist under metal pollution. However, both mechanisms are presumed to incur (energetic) costs and to trade-off with other life-history traits. To test this hypothesis, we exposed Pardosa saltans (Lycosidae) spiderlings originating from metal-polluted and unpolluted sites to a controlled cadmium (Cd) treatment, and compared contents of metal-binding metallothionein-like proteins (MTLPs), internal metal concentrations, and individual survival and growth rates with a reference treatment. While increased MTLP concentrations in offspring originating from both polluted and unpolluted populations upon exposure indicates a plastic tolerance mechanism, survival and growth rates remain largely unaffected, independent of the population of origin. However, MTLP and Cd concentrations were not significantly correlated. We suggest that MTLP production may be an important mechanism enabling P. saltans populations to persist in ecosystems polluted with heavy metals above a certain level. - Spiders from metal-polluted and unpolluted populations show a similar increase in MTLP production when exposed to Cd, with unaffected growth and survival.

  16. Neoadjuvant chemotherapy induces expression levels of breast cancer resistance protein that predict disease-free survival in breast cancer.

    Directory of Open Access Journals (Sweden)

    Baek Kim

    Full Text Available Three main xenobiotic efflux pumps have been implicated in modulating breast cancer chemotherapy responses. These are P-glycoprotein (Pgp, Multidrug Resistance-associated Protein 1 (MRP1, and Breast Cancer Resistance Protein (BCRP. We investigated expression of these proteins in breast cancers before and after neoadjuvant chemotherapy (NAC to determine whether their levels define response to NAC or subsequent survival. Formalin-fixed paraffin-embedded tissues were collected representing matched pairs of core biopsy (pre-NAC and surgical specimen (post-NAC from 45 patients with invasive ductal carcinomas. NAC regimes were anthracyclines +/- taxanes. Immunohistochemistry was performed for Pgp, MRP1 and BCRP and expression was quantified objectively using computer-aided scoring. Pgp and MRP1 were significantly up-regulated after exposure to NAC (Wilcoxon signed-rank p = 0.0024 and p<0.0001, while BCRP showed more variation in response to NAC, with frequent up- (59% of cases and down-regulation (41% contributing to a lack of significant difference overall. Pre-NAC expression of all markers, and post-NAC expression of Pgp and MRP1 did not correlate with NAC response or with disease-free survival (DFS. Post-NAC expression of BCRP did not correlate with NAC response, but correlated significantly with DFS (Log rank p = 0.007, with longer DFS in patients with low post-NAC BCRP expression. In multivariate Cox regression analyses, post-NAC BCRP expression levels proved to predict DFS independently of standard prognostic factors, with high expression associated with a hazard ratio of 4.04 (95% confidence interval 1.3-12.2; p = 0.013. We conclude that NAC-induced expression levels of BCRP predict survival after NAC for breast cancer, while Pgp and MRP1 expression have little predictive value.

  17. 10 year survival after breast-conserving surgery plus radiotherapy compared with mastectomy in early breast cancer in the Netherlands: a population-based study

    NARCIS (Netherlands)

    Maaren, M.C. van; Munck, L.; Bock, G.H. de; Jobsen, J.J.; Dalen, T. van; Linn, S.C.; Poortmans, P.; Strobbe, L.J.A.; Siesling, S.

    2016-01-01

    BACKGROUND: Investigators of registry-based studies report improved survival for breast-conserving surgery plus radiotherapy compared with mastectomy in early breast cancer. As these studies did not present long-term overall and breast cancer-specific survival, the effect of breast-conserving

  18. Comparative Analysis of Clinicopathologic Features of, Treatment in, and Survival of Americans with Lung or Bronchial Cancer.

    Directory of Open Access Journals (Sweden)

    Dan Li

    Full Text Available Ethnic disparities in lung and bronchial cancer diagnoses and disease-specific survival (DSS rates in the United States are well known. However, few studies have specifically assessed these differences in Asian subgroups. The primary objectives of the retrospective analysis described herein were to identify any significant differences in clinicopathologic features, treatment, and survival rate between Asian lung cancer patients and lung cancer patients in other broad ethnic groups in the United States and to determine the reasons for these differences among subgroups of Asian patients with lung or bronchial cancer. We searched the Surveillance, Epidemiology, and End Results Program database to identify patients diagnosed with lung or bronchial cancer from 1990 to 2012. Differences in clinicopathologic features, treatment, and DSS rate in four broad ethnic groups and eight Asian subgroups were compared. The study population consisted of 849,088 patients, 5.2% of whom were of Asian descent. Female Asian patients had the lowest lung and bronchial cancer incidence rates, whereas male black patients had the highest rates. Asian patients had the best 5-year DSS rate. In our Asian subgroup analysis, Indian/Pakistani patients had the best 5-year DSS rate, whereas Hawaiian/Pacific Islander patients had the worst 5-year DSS rates. We found the differences in DSS rate among the four broad ethnic groups and eight Asian subgroups when we grouped patients by age and disease stage, as well. Asian patients had better DSS rates than those in the other three broad ethnic groups in almost every age and disease-stage group, especially in older patients and those with advanced-stage disease. In conclusion, we found that clinicopathologic features and treatment of lung and bronchial cancer differ by ethnicity in the United States, and the differences impact survival in each ethnic group.

  19. COMPARATIVE PRODUCTION OF SINGLE CELL PROTEIN FROM FISH PROTEIN ISOLATE WASTAGE AND ULTRA FILTERED CHEESE WHEY

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    Soroush Haghighi-Manesh

    2013-02-01

    Full Text Available Fish protein isolate wastage and ultra filtered cheese whey were used as substrates for fermentation by Kluyveromyces marxianus to produce single cell protein, under batch and aerobic condition in which pH and temperature were adjusted to 4.5 and 35°C. The produced biomass was analyzed for protein content in different periods of time during fermentation. About 82% and 75% of total protein was produced in the first 18 h of 96 h fermentation of ultra filtered cheese whey and protein isolate wastage respectively, which can be an indication of the exponential phase of the yeast growth. The results of biomass yield measurements during 96 h process also confirm this finding. Moreover, since ultra filtered cheese whey was higher in single cell protein yield, solubility, water holding capacity, water absorption and power of biological and chemical oxygen demand reduction, and also was lower in foam overrun and stability than fish protein isolate wastage, it was selected as the suitable substrate for single cell protein production.

  20. Comparative transcriptional analysis of Bacillus subtilis cells overproducing either secreted proteins, lipoproteins or membrane proteins

    NARCIS (Netherlands)

    Marciniak, Bogumila C.; Trip, Hein; van-der Veek, Patricia J.; Kuipers, Oscar P.; Marciniak, Bogumiła C.

    2012-01-01

    Background: Bacillus subtilis is a favorable host for the production of industrially relevant proteins because of its capacity of secreting proteins into the medium to high levels, its GRAS (Generally Recognized As Safe) status, its genetic accessibility and its capacity to grow in large

  1. Statistical optimization of bambara groundnut protein isolate-alginate matrix systems on survival of encapsulated Lactobacillus rhamnosus GG

    Directory of Open Access Journals (Sweden)

    Kanyanat Kaewiad

    2017-08-01

    Full Text Available Encapsulation may protect viable probiotic cells. This study aims at the evaluation of a bambara groundnut protein isolate (BGPI-alginate matrix designed for encapsulating a probiotic Lactobacillus rhamnosus GG. The response surface methodology was employed to gain the optimal concentrations of BGPI and alginate on encapsulation efficiency and survival of encapsulated cells. The capsules were prepared at the optimal combination by the traditional extrusion method composed of 8.66% w/v BGPI and 1.85% w/v alginate. The encapsulation efficiency was 97.24%, whereas the survival rates in an acidic condition and after the freeze-drying process were 95.56% and 95.20%, respectively—higher than those using either BGPI or alginate as the encapsulating agent individually. The designed capsules increased the probiotic L. rhamnosus GG survival relative to free cells in a simulated gastric fluid by 5.00 log cfu/ml after 3 h and in a simulated intestinal fluid by 8.06 log cfu/ml after 4 h. The shelf-life studies of the capsules over 6 months at 4 °C and 30 °C indicated that the remaining number of viable cells in a BGPI-alginate capsule was significantly higher than that of free cells in both temperatures. It was demonstrated that the BGPI-alginate capsule could be utilized as a new probiotic carrier for enhanced gastrointestinal transit and storage applied in food and/or pharmaceutical products.

  2. EhMAPK, the mitogen-activated protein kinase from Entamoeba histolytica is associated with cell survival.

    Science.gov (United States)

    Ghosh, Anupama Sardar; Ray, Doel; Dutta, Suman; Raha, Sanghamitra

    2010-10-08

    Mitogen Activated Protein Kinases (MAPKs) are a class of serine/threonine kinases that regulate a number of different cellular activities including cell proliferation, differentiation, survival and even death. The pathogen Entamoeba histolytica possess a single homologue of a typical MAPK gene (EhMAPK) whose identification was previously reported by us but its functional implications remained unexplored. EhMAPK, the only mitogen-activated protein kinase from the parasitic protist Entamoeba histolytica with Threonine-X-Tyrosine (TXY) phosphorylation motif was cloned, expressed in E. coli and functionally characterized under different stress conditions. The expression profile of EhMAPK at the protein and mRNA level remained similar among untreated, heat shocked and hydrogen peroxide-treated samples in all cases of dose and time. But a significant difference was obtained in the phosphorylation status of the protein in response to different stresses. Heat shock at 43°C or 0.5 mM H(2)O(2) treatment enhanced the phosphorylation status of EhMAPK and augmented the kinase activity of the protein whereas 2.0 mM H(2)O(2) treatment induced dephosphorylation of EhMAPK and loss of kinase activity. 2.0 mM H(2)O(2) treatment reduced parasite viability significantly but heat shock and 0.5 mM H(2)O(2) treatment failed to adversely affect E. histolytica viability. Therefore, a distinct possibility that activation of EhMAPK is associated with stress survival in E. histolytica is seen. Our study also gives a glimpse of the regulatory mechanism of the protein under in vivo conditions. Since the parasite genome lacks any typical homologue of mammalian MEK, the dual specificity kinases which are the upstream activators of MAPK, indications of the existence of some alternate regulatory mechanisms of the EhMAPK activity is perceived. These may include the autophosphorylation activity of the protein itself in combination with some upstream phosphatases which are not yet identified.

  3. Lack of Outer Membrane Protein A Enhances the Release of Outer Membrane Vesicles and Survival of Vibrio cholerae and Suppresses Viability of Acanthamoeba castellanii

    Directory of Open Access Journals (Sweden)

    Soni Priya Valeru

    2014-01-01

    Full Text Available Vibrio cholerae, the causative agent of the diarrhoeal disease cholera, survives in aquatic environments. The bacterium has developed a survival strategy to grow and survive inside Acanthamoeba castellanii. It has been shown that V. cholerae expresses outer membrane proteins as virulence factors playing a role in the adherence to interacted host cells. This study examined the role of outer membrane protein A (OmpA and outer membrane vesicles (OMVs in survival of V. cholerae alone and during its interaction with A. castellanii. The results showed that an OmpA mutant of V. cholerae survived longer than wild-type V. cholerae when cultivated alone. Cocultivation with A. castellanii enhanced the survival of both bacterial strains and OmpA protein exhibited no effect on attachment, engulfment, and survival inside the amoebae. However, cocultivation of the OmpA mutant of V. cholerae decreased the viability of A. castellanii and this bacterial strain released more OMVs than wild-type V. cholerae. Surprisingly, treatment of amoeba cells with OMVs isolated from the OmpA mutant significantly decreased viable counts of the amoeba cells. In conclusion, the results might highlight a regulating rule for OmpA in survival of V. cholerae and OMVs as a potent virulence factor for this bacterium towards eukaryotes in the environment.

  4. Phosphatase and tensin homologue/protein kinase B pathway linked to motor neuron survival in human superoxide dismutase 1-related amyotrophic lateral sclerosis.

    Science.gov (United States)

    Kirby, Janine; Ning, Ke; Ferraiuolo, Laura; Heath, Paul R; Ismail, Azza; Kuo, Su-Wei; Valori, Chiara F; Cox, Laura; Sharrack, Basil; Wharton, Stephen B; Ince, Paul G; Shaw, Pamela J; Azzouz, Mimoun

    2011-02-01

    Gene expression profiling has been used previously with spinal cord homogenates and laser capture microdissected motor neurons to determine the mechanisms involved in neurodegeneration in amyotrophic lateral sclerosis. However, while cellular and animal model work has focused on superoxide dismutase 1-related amyotrophic lateral sclerosis, the transcriptional profile of human mutant superoxide dismutase 1 motor neurons has remained undiscovered. The aim of this study was to apply gene expression profiling to laser captured motor neurons from human superoxide dismutase 1-related amyotrophic lateral sclerosis and neurologically normal control cases, in order to determine those pathways dysregulated in human superoxide dismutase 1-related neurodegeneration and to establish potential pathways suitable for therapeutic intervention. Identified targets were then validated in cultured cell models using lentiviral vectors to manipulate the expression of key genes. Microarray analysis identified 1170 differentially expressed genes in spinal cord motor neurons from superoxide dismutase 1-related amyotrophic lateral sclerosis, compared with controls. These genes encoded for proteins in multiple functional categories, including those involved in cell survival and cell death. Further analysis determined that multiple genes involved in the phosphatidylinositol-3 kinase signalling cascade were differentially expressed in motor neurons that survived the disease process. Functional experiments in cultured cells and primary motor neurons demonstrate that manipulating this pathway by reducing the expression of a single upstream target, the negative phosphatidylinositol-3 kinase regulator phosphatase and tensin homology, promotes a marked pro-survival effect. Therefore, these data indicate that proteins in the phosphatidylinositol-3 kinase pathway could represent a target for therapeutic manipulation in motor neuron degeneration.

  5. Survival of metastatic melanoma patients after dendritic cell vaccination correlates with expression of leukocyte phosphatidylethanolamine-binding protein 1/Raf kinase inhibitory protein

    DEFF Research Database (Denmark)

    Buschow, Sonja I; Ramazzotti, Matteo; Reinieren-Beeren, Inge M J

    2017-01-01

    -scale microarray analysis of 74 samples from two treatment centers, taken directly after the first round of DC vaccination, was performed. We found that phosphatidylethanolamine binding protein 1 (PEBP1)/Raf Kinase inhibitory protein (RKIP) expression can be used to identify a significant proportion of patients......-based biomarkers are of particular interest because of their straightforward implementation in routine clinical care. We sought to identify markers for dendritic cell (DC) vaccine-based immunotherapy against metastatic melanoma through gene expression analysis of peripheral blood mononuclear cells. A large...... who performed poorly after DC vaccination. This result was validated by q-PCR analysis on blood samples from a second cohort of 95 patients treated with DC vaccination in four different centers. We conclude that low PEBP1 expression correlates with poor overall survival after DC vaccination...

  6. Spectrophotometric determination of total proteins in blood plasma: a comparative study among dye-binding methods

    OpenAIRE

    Dimas Augusto Morozin Zaia; Fábio Rangel Marques; Cássia Thaïs Bussamra Vieira Zaia

    2005-01-01

    A comparative study between the biuret method (standard method for total proteins) and spectrophotometric methods using dyes (Bradford, 3',3",5',5"-tetrabromophenolphthalein ethyl ester-TBPEE, and erythrosin-B) was carried out for the determination of total proteins in blood plasma from rats. Bradford method showed the highest sensitivity for proteins and biuret method showed the lowest. For all the methods, the absorbance for different proteins (BSA, casein, and egg albumin) was measured and...

  7. Unraveling novel broad-spectrum antibacterial targets in food and waterborne pathogens using comparative genomics and protein interaction network analysis.

    Science.gov (United States)

    Jadhav, Ankush; Shanmugham, Buvaneswari; Rajendiran, Anjana; Pan, Archana

    2014-10-01

    Food and waterborne diseases are a growing concern in terms of human morbidity and mortality worldwide, even in the 21st century, emphasizing the need for new therapeutic interventions for these diseases. The current study aims at prioritizing broad-spectrum antibacterial targets, present in multiple food and waterborne bacterial pathogens, through a comparative genomics strategy coupled with a protein interaction network analysis. The pathways unique and common to all the pathogens under study (viz., methane metabolism, d-alanine metabolism, peptidoglycan biosynthesis, bacterial secretion system, two-component system, C5-branched dibasic acid metabolism), identified by comparative metabolic pathway analysis, were considered for the analysis. The proteins/enzymes involved in these pathways were prioritized following host non-homology analysis, essentiality analysis, gut flora non-homology analysis and protein interaction network analysis. The analyses revealed a set of promising broad-spectrum antibacterial targets, present in multiple food and waterborne pathogens, which are essential for bacterial survival, non-homologous to host and gut flora, and functionally important in the metabolic network. The identified broad-spectrum candidates, namely, integral membrane protein/virulence factor (MviN), preprotein translocase subunits SecB and SecG, carbon storage regulator (CsrA), and nitrogen regulatory protein P-II 1 (GlnB), contributed by the peptidoglycan pathway, bacterial secretion systems and two-component systems, were also found to be present in a wide range of other disease-causing bacteria. Cytoplasmic proteins SecG, CsrA and GlnB were considered as drug targets, while membrane proteins MviN and SecB were classified as vaccine targets. The identified broad-spectrum targets can aid in the design and development of antibacterial agents not only against food and waterborne pathogens but also against other pathogens. Copyright © 2014 Elsevier B.V. All rights

  8. Analyses adjusting for selective crossover show improved overall survival with adjuvant letrozole compared with tamoxifen in the BIG 1-98 study

    DEFF Research Database (Denmark)

    Colleoni, Marco; Giobbie-Hurder, Anita; Regan, Meredith M

    2011-01-01

    Among postmenopausal women with endocrine-responsive breast cancer, the aromatase inhibitor letrozole, when compared with tamoxifen, has been shown to significantly improve disease-free survival (DFS) and time to distant recurrence (TDR). We investigated whether letrozole monotherapy prolonged...

  9. Comparative analysis of protein-protein interactions in the defense response of rice and wheat.

    Science.gov (United States)

    Cantu, Dario; Yang, Baoju; Ruan, Randy; Li, Kun; Menzo, Virginia; Fu, Daolin; Chern, Mawsheng; Ronald, Pamela C; Dubcovsky, Jorge

    2013-03-12

    Despite the importance of wheat as a major staple crop and the negative impact of diseases on its production worldwide, the genetic mechanisms and gene interactions involved in the resistance response in wheat are still poorly understood. The complete sequence of the rice genome has provided an extremely useful parallel road map for genetic and genomics studies in wheat. The recent construction of a defense response interactome in rice has the potential to further enhance the translation of advances in rice to wheat and other grasses. The objective of this study was to determine the degree of conservation in the protein-protein interactions in the rice and wheat defense response interactomes. As entry points we selected proteins that serve as key regulators of the rice defense response: the RAR1/SGT1/HSP90 protein complex, NPR1, XA21, and XB12 (XA21 interacting protein 12). Using available wheat sequence databases and phylogenetic analyses we identified and cloned the wheat orthologs of these four rice proteins, including recently duplicated paralogs, and their known direct interactors and tested 86 binary protein interactions using yeast-two-hybrid (Y2H) assays. All interactions between wheat proteins were further tested using in planta bimolecular fluorescence complementation (BiFC). Eighty three percent of the known rice interactions were confirmed when wheat proteins were tested with rice interactors and 76% were confirmed using wheat protein pairs. All interactions in the RAR1/SGT1/ HSP90, NPR1 and XB12 nodes were confirmed for the identified orthologous wheat proteins, whereas only forty four percent of the interactions were confirmed in the interactome node centered on XA21. We hypothesize that this reduction may be associated with a different sub-functionalization history of the multiple duplications that occurred in this gene family after the divergence of the wheat and rice lineages. The observed high conservation of interactions between proteins that

  10. Fluorescence-guided surgery of retroperitoneal-implanted human fibrosarcoma in nude mice delays or eliminates tumor recurrence and increases survival compared to bright-light surgery.

    Directory of Open Access Journals (Sweden)

    Fuminari Uehara

    Full Text Available The aim of this study is to determine if fluorescence-guided surgery (FGS can eradicate human fibrosarcoma growing in the retroperitoneum of nude mice. One week after retroperitoneal implantation of human HT1080 fibrosarcoma cells, expressing green fluorescent protein (GFP (HT-1080-GFP, in nude mice, bright-light surgery (BLS was performed on all tumor-bearing mice (n = 22. After BLS, mice were randomized into 2 treatment groups; BLS-only (n = 11 or the combination of BLS + FGS (n = 11. The residual tumors remaining after BLS were resected with FGS using a hand-held portable imaging system under fluorescence navigation. The average residual tumor area after BLS + FGS was significantly smaller than after BLS-only (0.4 ± 0.4 mm(2 and 10.5 ± 2.4 mm(2, respectively; p = 0.006. Five weeks after surgery, the fluorescent-tumor areas of BLS- and BLS + FGS-treated mice were 379 ± 147 mm(2 and 11.7 ± 6.9 mm(2, respectively, indicating that FGS greatly inhibited tumor recurrence compared to BLS. The combination of BLS + FGS significantly decreased fibrosarcoma recurrence compared to BLS-only treated mice (p < 0.001. Mice treated with BLS+FGS had a significantly higher disease-free survival rate than mice treated with BLS-only at five weeks after surgery. These results suggest that combination of BLS + FGS significantly reduced the residual fibrosarcoma volume after BLS and improved disease-free survival.

  11. Model-based estimates of annual survival rate are preferable to observed maximum lifespan statistics for use in comparative life-history studies

    Science.gov (United States)

    Krementz, D.G.; Sauer, J.R.; Nichols, J.D.

    1989-01-01

    Estimates of longevity are available for many animals, and are commonly used in comparative life-history analyses. We suggest that annual survival rate is more appropriate life history parameter for most comparative life history analyses. Observed maximum longevities were not correlated with the annual survival rate estimates and appear to be unstable over time. We recommend that observed maximum lifespans not be used in life history analyses.

  12. Survival in extreme environment by "preserve-expand-specialize" strategy: lessons from comparative genomics of an anhydrobiotic midge.

    Science.gov (United States)

    Gusev, Oleg; Sugimoto, Manabu; Novikova, Nataliya; Sychev, Vladimir; Okuda, Takashi; Kikawada, Takahiro

    2012-07-01

    Anhydrobiotic chironomid larvae of Polypedilum vanderplanki (Diptera) can withstand prolonged complete desiccation as well as other external stresses including ionizing radiation. Recent experiments showed that this insect is able to survive long-tern exposure to real outer space. At the same time, we found that dehydration causes alterations in chromatin structure and a severe fragmentation of nuclear DNA in the cells of the larvae despite successful anhydrobiosis. Analysis of several remote populations of the chironomid in Africa that desiccation-related DNA damage might be a driving genetic force for rapid radiation within the species. First results of ongoing genome project suggest that origin and evolution of anhydrobiosis in this single insect species related to rapid duplication of the genes, coding late embryogenesis abundant proteins (LEA) and other molecular agents directly involved in desiccation resistance in the cells. Analysis of genome-wide mRNA expression profiles in the larvae subjected to desiccation shows that joint-activity of large multiple-genes coding regions in the genome involved in control of anhydrobiosis-related molecular adaptations in the chironomid.

  13. Internationally comparable diagnosis-specific survival probabilities for calculation of the ICD-10-based Injury Severity Score

    DEFF Research Database (Denmark)

    Gedeborg, R.; Warner, M.; Chen, L. H.

    2014-01-01

    BACKGROUND: The International Statistical Classification of Diseases, 10th Revision (ICD-10) -based Injury Severity Score (ICISS) performs well but requires diagnosis-specific survival probabilities (DSPs), which are empirically derived, for its calculation. The objective was to examine if DSPs b...... based on data pooled from several countries could increase accuracy, precision, utility, and international comparability of DSPs and ICISS. METHODS: Australia, Argentina, Austria, Canada, Denmark, New Zealand, and Sweden provided ICD-10-coded injury hospital discharge data, including in......-hospital mortality status. Data from the seven countries were pooled using four different methods to create an international collaborative effort ICISS (ICE-ICISS). The ability of the ICISS to predict mortality using the country-specific DSPs and the pooled DSPs was estimated and compared. RESULTS: The pooled DSPs...... generated empirically derived DSPs. These pooled DSPs facilitate international comparisons and enables the use of ICISS in all settings where ICD-10 hospital discharge diagnoses are available. The modest reduction in performance of the ICE-ICISS compared with the country-specific scores is unlikely...

  14. Evaluation of serum biochemical marker concentrations and survival time in dogs with protein-losing enteropathy

    NARCIS (Netherlands)

    Equilino, Mirjam; Théodoloz, Vincent; Gorgas, Daniela; Doherr, Marcus G.; Heilmann, Romy M.; Suchodolski, Jan S.; Steiner, JöRg M.; Burgener, Iwan A.

    2015-01-01

    Results—Serum C-reactive protein concentration was high in 13 of 18 dogs with PLE and in 2 of 18 dogs with FRD. Serum concentration of canine pancreatic lipase immunoreactivity was high in 3 dogs with PLE but within the reference interval in all dogs with FRD. Serum a1-proteinase inhibitor

  15. Comparative Proteomics Provides Insights into Metabolic Responses in Rat Liver to Isolated Soy and Meat Proteins.

    Science.gov (United States)

    Song, Shangxin; Hooiveld, Guido J; Zhang, Wei; Li, Mengjie; Zhao, Fan; Zhu, Jing; Xu, Xinglian; Muller, Michael; Li, Chunbao; Zhou, Guanghong

    2016-04-01

    It has been reported that isolated dietary soy and meat proteins have distinct effects on physiology and liver gene expression, but the impact on protein expression responses are unknown. Because these may differ from gene expression responses, we investigated dietary protein-induced changes in liver proteome. Rats were fed for 1 week semisynthetic diets that differed only regarding protein source; casein (reference) was fully replaced by isolated soy, chicken, fish, or pork protein. Changes in liver proteome were measured by iTRAQ labeling and LC-ESI-MS/MS. A robust set totaling 1437 unique proteins was identified and subjected to differential protein analysis and biological interpretation. Compared with casein, all other protein sources reduced the abundance of proteins involved in fatty acid metabolism and Pparα signaling pathway. All dietary proteins, except chicken, increased oxidoreductive transformation reactions but reduced energy and essential amino acid metabolic pathways. Only soy protein increased the metabolism of sulfur-containing and nonessential amino acids. Soy and fish proteins increased translation and mRNA processing, whereas only chicken protein increased TCA cycle but reduced immune responses. These findings were partially in line with previously reported transcriptome results. This study further shows the distinct effects of soy and meat proteins on liver metabolism in rats.

  16. The survival of patients with Stage III Colon Cancer is improved in HNPCC compared with sporadic cases. A Danish registry based study

    DEFF Research Database (Denmark)

    Brixen, Line Merrild; Bernstein, Inge Thomsen; Bülow, Steffen

    2013-01-01

    AIM: Patients with hereditary non-polyposis colorectal cancer (HNPCC) seem to have a better prognosis than those with sporadic colon cancer (CC)s. The aim was to compare survival after stage III CC in patients with HNPCC with those having sporadic CC. METHOD: 230 patients with hereditary cancer...... history of cancer. Patient characteristics, geographic differences and survival data were analyzed. RESULTS: The overall survival (OS) was better in HNPCC patients compared to sporadic CC after stratification for sex and age (p=0.02; CI 1.04-1.7). The 5-year survival was 70% in HNPCC patients compared...... from The Danish HNPCC-Register and 3557 patients with sporadic CC from The Danish Colorectal Cancer Database, diagnosed during May 2001-December 2008 were included. HNPCC patients were classified according to Mismatch Repair mutation status and family pedigree. Sporadic cases had no known family...

  17. A comparative study of monoclonal antibodies. 1. Phase behavior and protein-protein interactions.

    Science.gov (United States)

    Lewus, Rachael A; Levy, Nicholas E; Lenhoff, Abraham M; Sandler, Stanley I

    2015-01-01

    Protein phase behavior is involved in numerous aspects of downstream processing, either by design as in crystallization or precipitation processes, or as an undesired effect, such as aggregation. This work explores the phase behavior of eight monoclonal antibodies (mAbs) that exhibit liquid-liquid separation, aggregation, gelation, and crystallization. The phase behavior has been studied systematically as a function of a number of factors, including solution composition and pH, in order to explore the degree of variability among different antibodies. Comparisons of the locations of phase boundaries show consistent trends as a function of solution composition; however, changing the solution pH has different effects on each of the antibodies studied. Furthermore, the types of dense phases formed varied among the antibodies. Protein-protein interactions, as reflected by values of the osmotic second virial coefficient, are used to correlate the phase behavior. The primary findings are that values of the osmotic second virial coefficient are useful for correlating phase boundary locations, though there is appreciable variability among the antibodies in the apparent strengths of the intrinsic protein-protein attraction manifested. However, the osmotic second virial coefficient does not provide a clear basis to predict the type of dense phase likely to result under a given set of solution conditions. © 2014 American Institute of Chemical Engineers.

  18. Fluorescence-guided surgery of retroperitoneal-implanted human fibrosarcoma in nude mice delays or eliminates tumor recurrence and increases survival compared to bright-light surgery.

    Science.gov (United States)

    Uehara, Fuminari; Hiroshima, Yukihiko; Miwa, Shinji; Tome, Yasunori; Yano, Shuya; Yamamoto, Mako; Matsumoto, Yasunori; Maehara, Hiroki; Tanaka, Kazuhiro; Bouvet, Michael; Kanaya, Fuminori; Hoffman, Robert M

    2015-01-01

    The aim of this study is to determine if fluorescence-guided surgery (FGS) can eradicate human fibrosarcoma growing in the retroperitoneum of nude mice. One week after retroperitoneal implantation of human HT1080 fibrosarcoma cells, expressing green fluorescent protein (GFP) (HT-1080-GFP), in nude mice, bright-light surgery (BLS) was performed on all tumor-bearing mice (n = 22). After BLS, mice were randomized into 2 treatment groups; BLS-only (n = 11) or the combination of BLS + FGS (n = 11). The residual tumors remaining after BLS were resected with FGS using a hand-held portable imaging system under fluorescence navigation. The average residual tumor area after BLS + FGS was significantly smaller than after BLS-only (0.4 ± 0.4 mm(2) and 10.5 ± 2.4 mm(2), respectively; p = 0.006). Five weeks after surgery, the fluorescent-tumor areas of BLS- and BLS + FGS-treated mice were 379 ± 147 mm(2) and 11.7 ± 6.9 mm(2), respectively, indicating that FGS greatly inhibited tumor recurrence compared to BLS. The combination of BLS + FGS significantly decreased fibrosarcoma recurrence compared to BLS-only treated mice (p fibrosarcoma volume after BLS and improved disease-free survival.

  19. WEBnm@ v2.0: Web server and services for comparing protein flexibility.

    Science.gov (United States)

    Tiwari, Sandhya P; Fuglebakk, Edvin; Hollup, Siv M; Skjærven, Lars; Cragnolini, Tristan; Grindhaug, Svenn H; Tekle, Kidane M; Reuter, Nathalie

    2014-12-30

    Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma . WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.

  20. Comparative Molecular Dynamics Simulations of Mitogen-Activated Protein Kinase-Activated Protein Kinase 5

    Directory of Open Access Journals (Sweden)

    Inger Lindin

    2014-03-01

    Full Text Available The mitogen-activated protein kinase-activated protein kinase MK5 is a substrate of the mitogen-activated protein kinases p38, ERK3 and ERK4. Cell culture and animal studies have demonstrated that MK5 is involved in tumour suppression and promotion, embryogenesis, anxiety, cell motility and cell cycle regulation. In the present study, homology models of MK5 were used for molecular dynamics (MD simulations of: (1 MK5 alone; (2 MK5 in complex with an inhibitor; and (3 MK5 in complex with the interaction partner p38α. The calculations showed that the inhibitor occupied the active site and disrupted the intramolecular network of amino acids. However, intramolecular interactions consistent with an inactive protein kinase fold were not formed. MD with p38α showed that not only the p38 docking region, but also amino acids in the activation segment, αH helix, P-loop, regulatory phosphorylation region and the C-terminal of MK5 may be involved in forming a very stable MK5-p38α complex, and that p38α binding decreases the residual fluctuation of the MK5 model. Electrostatic Potential Surface (EPS calculations of MK5 and p38α showed that electrostatic interactions are important for recognition and binding.

  1. Comparative Proteomic Analysis of Mycobacterium tuberculosis Lineage 7 and Lineage 4 Strains Reveals Differentially Abundant Proteins Linked to Slow Growth and Virulence

    Directory of Open Access Journals (Sweden)

    Solomon A. Yimer

    2017-05-01

    Full Text Available In order to decipher the nature of the slowly growing Mycobacterium tuberculosis (M.tuberculosis lineage 7, the differentially abundant proteins in strains of M. tuberculosis lineage 7 and lineage 4 were defined. Comparative proteomic analysis by mass spectrometry was employed to identify, quantitate and compare the protein profiles of strains from the two M. tuberculosis lineages. Label-free peptide quantification of whole cells from M. tuberculosis lineage 7 and 4 yielded the identification of 2825 and 2541 proteins, respectively. A combined total of 2867 protein groups covering 71% of the predicted M. tuberculosis proteome were identified. The abundance of 125 proteins in M. tuberculosis lineage 7 and 4 strains was significantly altered. Notably, the analysis showed that a number of M. tuberculosis proteins involved in growth and virulence were less abundant in lineage 7 strains compared to lineage 4. Five ABC transporter proteins, three phosphate binding proteins essential for inorganic phosphate uptake, and six components of the type 7 secretion system ESX-3 involved in iron acquisition were less abundant in M. tuberculosis lineage 7. This proteogenomic analysis provided an insight into the lineage 7-specific protein profile which may provide clues to understanding the differential properties of lineage 7 strains in terms of slow growth, survival fitness, and pathogenesis.

  2. Human DNA Glycosylase NEIL1’s Interactions with Downstream Repair Proteins Is Critical for Efficient Repair of Oxidized DNA Base Damage and Enhanced Cell Survival

    Directory of Open Access Journals (Sweden)

    Istvan Boldogh

    2012-11-01

    Full Text Available NEIL1 is unique among the oxidatively damaged base repair-initiating DNA glycosylases in the human genome due to its S phase-specific activation and ability to excise substrate base lesions from single-stranded DNA. We recently characterized NEIL1’s specific binding to downstream canonical repair and non-canonical accessory proteins, all of which involve NEIL1’s disordered C-terminal segment as the common interaction domain (CID. This domain is dispensable for NEIL1’s base excision and abasic (AP lyase activities, but is required for its interactions with other repair proteins. Here, we show that truncated NEIL1 lacking the CID is markedly deficient in initiating in vitro repair of 5-hydroxyuracil (an oxidative deamination product of C in a plasmid substrate compared to the wild-type NEIL1, thus suggesting a critical role of CID in the coordination of overall repair. Furthermore, while NEIL1 downregulation significantly sensitized human embryonic kidney (HEK 293 cells to reactive oxygen species (ROS, ectopic wild-type NEIL1, but not the truncated mutant, restored resistance to ROS. These results demonstrate that cell survival and NEIL1-dependent repair of oxidative DNA base damage require interactions among repair proteins, which could be explored as a cancer therapeutic target in order to increase the efficiency of chemo/radiation treatment.

  3. Ovarian cancer survival population differences: a "high resolution study" comparing Philippine residents, and Filipino-Americans and Caucasians living in the US

    Directory of Open Access Journals (Sweden)

    Uy Gemma

    2009-09-01

    Full Text Available Abstract Background In contrast to most other forms of cancer, data from some developing and developed countries show surprisingly similar survival rates for ovarian cancer. We aimed to compare ovarian cancer survival in Philippine residents, Filipino-Americans and Caucasians living in the US, using a high resolution approach, taking potential differences in prognostic factors into account. Methods Using databases from the SEER 13 and from the Manila and Rizal Cancer Registries, age-adjusted five-year absolute and relative survival estimates were computed using the period analysis method and compared between Filipino-American ovarian cancer patients with cancer patients from the Philippines and Caucasians in the US. Cox proportional hazards modelling was used to determine factors affecting survival differences. Results Despite more favorable distribution of age and cancer morphology and similar stage distribution, 5-year absolute and relative survival were lower in Philippine residents (Absolute survival, AS, 44%, Standard Error, SE, 2.9 and Relative survival, RS, 49.7%, SE, 3.7 than in Filipino-Americans (AS, 51.3%, SE, 3.1 and RS, 54.1%, SE, 3.4. After adjustment for these and additional covariates, strong excess risk of death for Philippine residents was found (Relative Risk, RR, 2.45, 95% confidence interval, 95% CI, 1.99-3.01. In contrast, no significant differences were found between Filipino-Americans and Caucasians living in the US. Conclusion Multivariate analyses disclosed strong survival disadvantages of Philippine residents compared to Filipino-American patients, for which differences in access to health care might have played an important role. Survival is no worse among Filipino-Americans than among Caucasians living in the US.

  4. Targeting the Pro-Survival Protein MET with Tivantinib (ARQ 197) Inhibits Growth of Multiple Myeloma Cells12

    Science.gov (United States)

    Zaman, Shadia; Shentu, Shujun; Yang, Jing; He, Jin; Orlowski, Robert Z.; Stellrecht, Christine M.; Gandhi, Varsha

    2015-01-01

    The hepatocyte growth factor (HGF)/MNNG HOS transforming gene (MET) pathway regulates cell growth, survival, and migration. MET is mutated or amplified in several malignancies. In myeloma, MET is not mutated, but patients have high plasma concentrations of HGF, high levels of MET expression, and gene copy number, which are associated with poor prognosis and advanced disease. Our previous studies demonstrated that MET is critical for myeloma cell survival and its knockdown induces apoptosis. In our current study, we tested tivantinib (ARQ 197), a small-molecule pharmacological MET inhibitor. At clinically achievable concentrations, tivantinib induced apoptosis by > 50% in all 12 human myeloma cell lines tested. This biologic response was associated with down-regulation of MET signaling and inhibition of the mitogen-activated protein kinase and phosphoinositide 3-kinase pathways, which are downstream of the HGF/MET axis. Tivantinib was equally effective in inducing apoptosis in myeloma cell lines resistant to standard chemotherapy (melphalan, dexamethasone, bortezomib, and lenalidomide) as well as in cells that were co-cultured with a protective bone marrow microenvironment or with exogenous cytokines. Tivantinib induced apoptosis in CD138 + plasma cells from patients and demonstrated efficacy in a myeloma xenograft mouse model. On the basis of these data, we initiated a clinical trial for relapsed/refractory multiple myeloma (MM). In conclusion, MET inhibitors may be an attractive target-based strategy for the treatment of MM. PMID:25810013

  5. Targeting the pro-survival protein MET with tivantinib (ARQ 197) inhibits growth of multiple myeloma cells.

    Science.gov (United States)

    Zaman, Shadia; Shentu, Shujun; Yang, Jing; He, Jin; Orlowski, Robert Z; Stellrecht, Christine M; Gandhi, Varsha

    2015-03-01

    The hepatocyte growth factor (HGF)/MNNG HOS transforming gene (MET) pathway regulates cell growth, survival, and migration. MET is mutated or amplified in several malignancies. In myeloma, MET is not mutated, but patients have high plasma concentrations of HGF, high levels of MET expression, and gene copy number, which are associated with poor prognosis and advanced disease. Our previous studies demonstrated that MET is critical for myeloma cell survival and its knockdown induces apoptosis. In our current study, we tested tivantinib (ARQ 197), a small-molecule pharmacological MET inhibitor. At clinically achievable concentrations, tivantinib induced apoptosis by >50% in all 12 human myeloma cell lines tested. This biologic response was associated with down-regulation of MET signaling and inhibition of the mitogen-activated protein kinase and phosphoinositide 3-kinase pathways, which are downstream of the HGF/MET axis. Tivantinib was equally effective in inducing apoptosis in myeloma cell lines resistant to standard chemotherapy (melphalan, dexamethasone, bortezomib, and lenalidomide) as well as in cells that were co-cultured with a protective bone marrow microenvironment or with exogenous cytokines. Tivantinib induced apoptosis in CD138+ plasma cells from patients and demonstrated efficacy in a myeloma xenograft mouse model. On the basis of these data, we initiated a clinical trial for relapsed/refractory multiple myeloma (MM). In conclusion, MET inhibitors may be an attractive target-based strategy for the treatment of MM. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Impact of XIAP protein levels on the survival of myeloma cells

    Science.gov (United States)

    Desplanques, Grégoire; Giuliani, Nicola; Delsignore, Roberto; Rizzoli, Vittorio; Bataille, Régis; Barillé-Nion, Sophie

    2009-01-01

    Background XIAP is the best characterized and the most potent direct endogenous caspase inhibitor and is considered a key actor in the control of apoptotic threshold in cancer cells. In this report, we specifically addressed XIAP regulation and function in myeloma cells. Design and Methods XIAP and its endogenous inhibitor XAF-1 protein levels and their regulation were assessed by immunoblot analysis in myeloma cell lines or primary myeloma cells. XIAP knockdown by RNA interference was used to evaluate XIAP impact on in vitro drug sensitivity and in vivo tumor growth. Results Our results indicate that myeloma cells expressed high levels of XIAP protein that were tightly regulated during growth factor stimulation or stress condition. Of note, an increased XIAPlevel was evidenced during the blockade of the canonical cap-dependent translation by the mTOR inhibitor rapamycin, supporting the hypothesis of a functional IRES sequence in XIAP mRNA. In addition, caspase-mediated XIAP cleavage correlated to an apoptotic process occurring upon cell treatment with the proteasome inhibitor bortezomib. Importantly, XIAP knockdown using RNA interference enhanced drug sensitivity and decreased tumor formation in NOD/SCID mice. Finally, myeloma cells also expressed the XIAP inhibitor XAF-1 that interacted with XIAP in viable myeloma cells. Conclusions Altogether, our data argue for a delicate control of XIAP function in myeloma cells and stimulate interest in targeting XIAP in myeloma treatment. PMID:19001278

  7. Comparative Survival Study (CSS) of PIT-Tagged Spring/Summer Chinook and Summer Steelhead : 2008 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Comparative Survival Study Oversight Committee and Fish Passage Center

    2008-12-02

    The Comparative Survival Study (CSS; BPA Project 199602000) began in 1996 with the objective of establishing a long term dataset of the survival rate of annual generations of salmon from their outmigration as smolts to their return to freshwater as adults to spawn (smolt-to-adult return rate; SAR). The study was implemented with the express need to address the question whether collecting juvenile fish at dams and transporting them downstream in barges and trucks and releasing them downstream of Bonneville Dam was compensating for the effect of the Federal Columbia River Power System (FCRPS) on survival of Snake Basin spring/summer Chinook salmon migrating through the hydrosystem. The Completion of this annual report for the CSS signifies the 12th outmigration year of hatchery spring/summer Chinook salmon marked with Passive Integrated Transponder (PIT) tags as part of the CSS and the 9th complete brood year return as adults of those PIT-tagged fish (report covers adult returns from 1997-2006 hatchery Chinook juvenile migrations). In addition, the CSS has provided PIT-tags to on-going tagging operations for wild Chinook since 2002 (report covers adult returns from 1994-2006 wild Chinook juvenile migrations). The CSS tags wild steelhead on the lower Clearwater River and utilized wild and hatchery steelhead from other tagging operations in evaluations of transportation (report covers adult returns from 1997-2005 wild and hatchery steelhead migrations). The primary purpose of this report is to update the time series of smolt-to-adult survival rate data and related parameters with additional years of data since the completion of the CSS 10-yr retrospective analysis report (Schaller et al 2007). The 10-yr report provided a synthesis of the results from this ongoing study, the analytical approaches employed, and the evolving improvements incorporated into the study as reported in CSS annual progress reports. This current report specifically addresses the constructive

  8. Association of p53 protein expression with responses and survival of patients with locally advanced esophageal carcinoma treated with chemoradiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Muro, Kei; Ohtsu, Atsushi; Boku, Narikazu; Chin, Keisho; Oda, Yasushi; Fujii, Takahiro; Hosokawa, Koichi; Yoshida, Shigeaki [National Cancer Center Hospital East, Kashiwa, Chiba (Japan); Hasebe, Takahiro

    1996-04-01

    Immunohistochemical analysis was performed to determine the clinical role of p53 mutations in patients with locally advanced esophageal carcinomas treated with concurrent chemoradiotherapy. The subjects of this study were 20 patients with previously untreated esophageal carcinomas with evidence of T4 disease and/or distant node metastases. Treatment comprised protracted 5-fluorouracil and 2-h cisplatinum infusions along with radiation treatment with a total radiation dose of 60 Gy. Tumor specimens from 18 of the 20 patients were analyzed immunohistochemically. Mutant p53 protein expression in the biopsy materials from the primary tumors was analyzed by immunohistochemical staining using a polyclonal antibody, RSP53. Expression of p53 was detected immunohistochemically in 10 (56%) of the 18 esophageal tumors, the cancer cell nuclei of which were diffusely stained. There were no significant differences between the patient backgrounds of the p53-`positive` and `negative` groups. Four (40%) of the 10 patients with p53 expression achieved overall complete remissions (CRs) and 7 (70%) of these 10 achieved CRs of their primary tumors. In contrast, none of the 8 p53-negative patients achieved overall CRs and two (25%) achieved CRs of their primary tumors. The CR rates overall and of primary tumors tended to be higher in the p53-positive than negative group, but the differences were not significant. The survival rate for the 10 patients with p53 expression was better than that for the 8 negative ones (P>0.01): their median survival times were 12 and 4.5 months, respectively. Expression of p53 protein may be an indicator of a favorable prognosis in patients with locally advanced esophageal carcinomas treated with concurrent chemoradiotherapy. (author).

  9. Expression of CUB domain containing protein (CDCP1) is correlated with prognosis and survival of patients with adenocarcinoma of lung.

    Science.gov (United States)

    Ikeda, Jun-ichiro; Oda, Tomofumi; Inoue, Masayoshi; Uekita, Takamasa; Sakai, Ryuichi; Okumura, Meinoshin; Aozasa, Katsuyuki; Morii, Eiichi

    2009-03-01

    CUB domain containing protein (CDCP1), a transmembrane protein with intracellular tyrosine residues which are phosphorylated upon activation, is supposed to be engaged in proliferative activities and resistance to apoptosis of cancer cells. Expression level of CDCP1 was examined in lung adenocarcinoma, and its clinical implications were evaluated. CDCP1 expression was immunohistochemically examined in lung adenocarcinoma from 200 patients. Staining intensity of cancer cells was categorized as low and high in cases with tumor cells showing no or weak and strong membrane staining, respectively. MIB-1 labeling index was also examined. There were 113 males and 87 females with median age of 63 years. Stage of disease was stage I in 144 cases (72.0%), II in 19 (9.5%), and III in 37 (18.5%). Sixty of 200 cases (30.0%) were categorized as CDCP1-high, and the remaining as CDCP1-low. Significant positive correlation was observed between CDCP1-high expression and relapse rate (P < 0.0001), poor prognosis (P < 0.0001), MIB-1 labeling index (P < 0.0001), and occurrence of lymph node metastasis (P = 0.0086). There was a statistically significant difference in disease-free survival (DFS) (P < 0.0001) and overall survival (OS) rates (P < 0.0001) between patients with CDCP1-high and CDCP1-low tumors. Univariate analysis showed that lymph node status, tumor stage, and CDCP1 expression were significant factors for both OS and DFS. Multivariate analysis revealed that only CDCP1 expression was an independent prognostic factor for both OS and DFS. CDCP1 expression level is a useful marker for prediction of patients with lung adenocarcinoma

  10. Immunogenicity of recombinant porcine attaching and effacing-associated protein compared with intimin fragment in Escherichia coli O157:H7-infected mice.

    Science.gov (United States)

    Li, Tao; Han, Ran; Wang, Qin; Wang, Shenghan; Fang, Huali; Li, Zhan; Tu, Wei; Wang, Dehui; Wang, Hui

    2013-12-01

    Enterohemorrhagic Escherichia coli (EHEC) causes a wide spectrum of food- and waterborne infectious diseases, including diarrhea, hemorrhagic colitis, and even hemolytic-uremic syndrome. Porcine attaching and effacing-associated protein (Paa) was first identified in a porcine enteropathogenic E. coli strain. It has been proven essential in the attaching and effacing mechanism of EHEC. However, the immunologic function of the Paa protein has yet to be established. In the present study, recombinant Paa protein was overexpressed successfully in engineered E. coli and effectively purified to homogeneity. Comparative experiments were carried out in mice with a known adhesion factor (intimin) as reference to investigate the immunogenicity of Paa. Intraperitoneal immunization of Paa protein in mice elicited significantly high levels of serum immunoglobulin G antibodies via Th2-mediated humoral immune response. In mice challenged with E. coli O157:H7, Paa protein exhibited immunological effectiveness against pathogenic bacteria colonization and excretion in vivo. Compared with the intimin, Paa showed better protective effect against E. coli O157:H7 infection in mice, particularly those challenged with high lethal doses of the pathogen. Seventy percent of the mice challenged with 50 minimal lethal dose (MLD) in the Paa group survived, whereas only 50% survived in the intimin group. This finding is the first description of the immunologic function of the Paa protein. These attributes provide support for the development of Paa-based vaccine, which can be beneficial in treating infectious diseases caused by E. coli O157:H7.

  11. A docking study of enhanced intracellular survival protein from Mycobacterium tuberculosis with human DUSP16/MKP-7

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Hye-Jin, E-mail: yoonhj@snu.ac.kr; Kim, Kyoung Hoon [Seoul National University, Seoul 151-747 (Korea, Republic of); Yang, Jin Kuk [Soongsil University, Seoul 156-743 (Korea, Republic of); Suh, Se Won [Seoul National University, Seoul 151-747 (Korea, Republic of); Seoul National University, Seoul 151-747 (Korea, Republic of); Kim, Hyunsik; Jang, Soonmin, E-mail: yoonhj@snu.ac.kr [Sejong University, Seoul 143-747 (Korea, Republic of)

    2013-11-01

    A docking study of Mtb Eis with its substrate DUSP16/MKP-7 was performed. The docking model suggests dissociation of hexameric Mtb Eis into dimers or monomers. The intracellular pathogen Mycobacterium tuberculosis (Mtb) causes tuberculosis, and one of its secreted effector proteins, called enhanced intracellular survival (Eis) protein, enhances its survival in macrophages. Mtb Eis activates JNK-specific dual-specificity protein phosphatase 16 (DUSP16)/mitogen-activated protein kinase phosphatase-7 (MKP-7) through the acetylation on Lys55, thus inactivating JNK by dephosphorylation. Based on the recently reported crystal structure of Mtb Eis, a docking model for the binding of Mtb Eis to DUSP16/MKP-7 was generated. In the docking model, the substrate helix containing Lys55 of DUSP16/MKP-7 fits nicely into the active-site cleft of Mtb Eis; the twisted β-sheet of Eis domain II embraces the substrate helix from one side. Most importantly, the side-chain of Lys55 is inserted toward acetyl-CoA and the resulting distance is 4.6 Å between the NZ atom of Lys55 and the carbonyl carbon of the acetyl group in acetyl-CoA. The binding of Mtb Eis and DUSP16/MKP-7 is maintained by strong electrostatic interactions. The active-site cleft of Mtb Eis has a negatively charged surface formed by Asp25, Glu138, Asp286, Glu395 and the terminal carboxylic group of Phe396. In contrast, DUSP16/MKP-7 contains five basic residues, Lys52, Lys55, Arg56, Arg57 and Lys62, which point toward the negatively charged surface of the active-site pocket of Mtb Eis. Thus, the current docking model suggests that the binding of DUSP16/MKP-7 to Mtb Eis should be established by charge complementarity in addition to a very favorable geometric arrangement. The suggested mode of binding requires the dissociation of the hexameric Mtb Eis into dimers or monomers. This study may be useful for future studies aiming to develop inhibitors of Mtb Eis as a new anti-tuberculosis drug candidate.

  12. Comparative Analysis of Electrophoretic Profile of Major Proteins of Milk from Alpine and Carpathian Goats

    OpenAIRE

    Alina NASALEAN; Laurentiu OGNEAN; Sergiu MUNTEAN; Stefana BALICI; MATEI, HOREA

    2017-01-01

    The milk’s proteins provide nutritional and biologically active values, essential in human and animal nutrition. In the case of goat milk, the proteins’ concentration and quality represent basic indices for the evaluation of the nutritional and biologically active values. The proposal is to comparatively analyse the protein profile of milk. The milk was collected from two different breeds: French Alpine and Romanian Carpathian. During March and April 2016 there were collected samples of r...

  13. Comparative Proteome Analysis in Schizosaccharomyces pombe Identifies Metabolic Targets to Improve Protein Production and Secretion.

    Science.gov (United States)

    Hung, Chien-Wen; Klein, Tobias; Cassidy, Liam; Linke, Dennis; Lange, Sabrina; Anders, Uwe; Bureik, Matthias; Heinzle, Elmar; Schneider, Konstantin; Tholey, Andreas

    2016-10-01

    Protein secretion in yeast is a complex process and its efficiency depends on a variety of parameters. We performed a comparative proteome analysis of a set of Schizosaccharomyces pombe strains producing the α-glucosidase maltase in increasing amounts to investigate the overall proteomic response of the cell to the burden of protein production along the various steps of protein production and secretion. Proteome analysis of these strains, utilizing an isobaric labeling/two dimensional LC-MALDI MS approach, revealed complex changes, from chaperones and secretory transport machinery to proteins controlling transcription and translation. We also found an unexpectedly high amount of changes in enzyme levels of the central carbon metabolism and a significant up-regulation of several amino acid biosyntheses. These amino acids were partially underrepresented in the cellular protein compared with the composition of the model protein. Additional feeding of these amino acids resulted in a 1.5-fold increase in protein secretion. Membrane fluidity was identified as a second bottleneck for high-level protein secretion and addition of fluconazole to the culture caused a significant decrease in ergosterol levels, whereas protein secretion could be further increased by a factor of 2.1. In summary, we show that high level protein secretion causes global changes of protein expression levels in the cell and that precursor availability and membrane composition limit protein secretion in this yeast. In this respect, comparative proteome analysis is a powerful tool to identify targets for an efficient increase of protein production and secretion in S. pombe Data are available via ProteomeXchange with identifiers PXD002693 and PXD003016. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Comparative properties of the Charcot-Leyden crystal protein and the major basic protein from human eosinophils.

    Science.gov (United States)

    Gleich, G J; Loegering, D A; Mann, K G; Maldonado, J E

    1976-01-01

    Guinea pig eosinophil granules contain a protein, the major basic protein (MBP), which accounts for more than half of the total granule protein, has a high content of arginine, and displays a remarkable tendency to form disulfide-linked aggregates. In this study we have purified a similar protein from human eosinophil granules and have compared the human MBP to the protein comprising the Charcot-Leyden crystal (CLC). Eosinophils from patients with various diseases were purified and disrupted, and the granule fraction was obtained. Examination of the granule fraction by transmission electron microscopy showed numerous typical eosinophil granules. Analyses of granule lysates by gel filtration and by polyacrylamide gel electrophoresis revealed the presence of peroxidase and MBP with properties similar to that previously found in guinea pig eosinophil granules. The human MBP had a molecular weight of 9,200, contained less than 1% carbohydrate, was rich in arginine, and readily formed disulfide-bonded aggregates. CLC were prepared from eosinophil-rich cell suspensions by homogenization in hypotonic saline. The supernates following centrifugation of cell debris spontaneously formed CLC. Analysis of CLC revealed the presence of a protein with a molecular weight of 13,000 containing 1.2% carbohydrate. The protein displayed a remarkable tendency to aggregate even in the presence of 0.2 M acetic acid. Human MBP and CLC protein differed in their molecular weights, carbohydrate compositions, and amino acid analyses. Mixtures of the MBP and the CLC protein yielded two bands in polyacrylamide gel electrophoresis. Neither eosinophil protein increased vascular permeability in the guinea pig skin or contracted the guinea pig ileum. The results indicate that the human MBP and the CLC are distinct substances with properties such that one cannot be derived from the other. Images PMID:942977

  15. Patterns of care and survival of glioblastoma patients: a comparative study between 2004 and 2008 in Lyon, France.

    Science.gov (United States)

    Badaoui, N; Meyronet, D; Cartalat-Carel, S; Guyotat, J; Jouanneau, E; d'Hombres, A; Sunyach, M P; Jouvet, A; Louis-Tisserand, G; Archinet, A; Frappaz, D; Bauchet, L; Honnorat, J; Ducray, F

    2014-03-01

    The treatment of glioblastomas (GBMs) has changed significantly since 2005. However, the extent to which this change has improved overall survival (OS) of patients treated outside clinical trials remains to be determined. We compared the patterns of care and OS of all GBM patients diagnosed in 2004 (n=105) and in 2008 (n=130) in our center. Younger patients (aged<70 years) diagnosed in 2008 received temozolomide radiochemotherapy as the initial treatment and bevacizumab at recurrence more frequently than those diagnosed in 2004 (69% vs 26% P<10(-4) and 41% vs 3%, P<10(-4), respectively). Elderly patients (aged≥70 years) diagnosed in 2008 received an oncological treatment (radiotherapy and/or chemotherapy) more frequently than those diagnosed in 2004 (67% vs 38%, P=0.006). The patients diagnosed in 2008 had longer OS than those diagnosed in 2004 (10.5 months vs 5.3 months, P=0.001). This finding was true for both younger and elderly patients (15.3 months vs 8.9 months, P=0.02 and 6.4 months vs 3.2 months, P=0.0002, respectively) and when considering only IDH1 wild-type patients (8.9 months vs 5.3 months, P=0.004). In our center, the change in the patterns of care for GBMs between 2004 and 2008 has been associated with a significant improvement in OS. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  16. Comparing human-Salmonella with plant-Salmonella protein-protein interaction predictions

    Directory of Open Access Journals (Sweden)

    Sylvia eSchleker

    2015-01-01

    Full Text Available Salmonellosis is the most frequent food-borne disease world-wide and can be transmitted to humans by a variety of routes, especially via animal and plant products. Salmonella bacteria are believed to use not only animal and human but also plant hosts despite their evolutionary distance. This raises the question if Salmonella employs similar mechanisms in infection of these diverse hosts. Given that most of our understanding comes from its interaction with human hosts, we investigate here to what degree knowledge of Salmonella-human interactions can be transferred to the Salmonella-plant system. Reviewed are recent publications on analysis and prediction of Salmonella-host interactomes. Putative protein-protein interactions (PPIs between Salmonella and its human and Arabidopsis hosts were retrieved utilizing purely interolog-based approaches in which predictions were inferred based on available sequence and domain information of known PPIs, and machine learning approaches that integrate a larger set of useful information from different sources. Transfer learning is an especially suitable machine learning technique to predict plant host targets from the knowledge of human host targets. A comparison of the prediction results with transcriptomic data shows a clear overlap between the host proteins predicted to be targeted by PPIs and their gene ontology enrichment in both host species and regulation of gene expression. In particular, the cellular processes Salmonella interferes with in plants and humans are catabolic processes. The details of how these processes are targeted, however, are quite different between the two organisms, as expected based on their evolutionary and habitat differences. Possible implications of this observation on evolution of host-pathogen communication are discussed.

  17. Single- versus Triple-Drug Chemoembolization for Hepatocellular Carcinoma: Comparing Outcomes by Toxicity, Imaging Response, and Survival.

    Science.gov (United States)

    Mouli, Samdeep K; Hickey, Ryan; Thornburg, Bartley; Sato, Kent T; Desai, Kush; Gabr, Ahmed; Kallini, Joseph R; Niemeri, Halla; Kircher, Sheetal; Mulcahy, Mary F; Benson Iii, Al B; Gupta, Ramona; Salem, Riad; Lewandowski, Robert J

    2016-09-01

    To determine the efficacy of single- versus triple-drug chemoembolization for the treatment of hepatocellular carcinoma, as measured by toxicity, tumor response, time to progression (TTP), and overall survival (OS). A single-center retrospective review was performed on 337 patients who underwent chemoembolization over a 14-year period; 172 patients underwent triple-drug conventional transarterial chemoembolization, and 165 patients underwent single-agent doxorubicin chemoembolization. Imaging characteristics and clinical follow-up after conventional transarterial chemoembolization were evaluated to determine TTP. Imaging response was determined per World Health Organization and European Association for the Study of Liver criteria. OS from time of first chemoembolization was calculated. Median TTP was similar between groups: 7.9 months (95% confidence interval [CI], 7.1-9.4) and 6.8 months (95% CI, 4.6-8.6) for triple- and single-drug regimens, respectively (P > .05). For single-agent conventional transarterial chemoembolization, median OS varied significantly by Barcelona Clinic for Liver Cancer (BCLC) stage: A, 40.8 months; B, 36.4 months; C, 10.9 months (P < .01). Median OS for triple-drug therapy also varied significantly by BCLC: A, 28.9 months; B, 18.1 months; C, 9.0 months (P < .01). Single-drug conventional transarterial chemoembolization demonstrated longer median OS compared with triple-drug therapy (P < .05) for BCLC A/B patients. Single-agent chemoembolization with doxorubicin and ethiodized oil demonstrates acceptable efficacy as measured by TTP and OS. Results compare favorably with traditional triple-drug therapy. Copyright © 2016 SIR. Published by Elsevier Inc. All rights reserved.

  18. Baseline C-reactive protein is associated with incident cancer and survival in patients with cancer

    DEFF Research Database (Denmark)

    Allin, Kristine H; Bojesen, Stig E; Nordestgaard, Børge G

    2009-01-01

    PURPOSE: We tested the hypothesis that baseline plasma levels of C-reactive protein (CRP) are associated with risk of incident cancer in the general population and early death in patients with cancer. PATIENTS AND METHODS: A total of 10,408 individuals from the Danish general population who had CRP...... measured at baseline were observed for up to 16 years; 1,624 developed cancer, and of these, 998 patients died during follow-up. Follow-up was 100% complete. We excluded individuals with a cancer diagnosis at baseline. RESULTS: Baseline CRP levels more than 3 versus less than 1 mg/L were associated...... with multifactorially adjusted hazard ratios of 1.3 (95% CI, 1.0 to 1.6) for cancer of any type, 2.2 (95% CI, 1.0 to 4.6) for lung cancer, 1.9 (95% CI, 0.8 to 4.6) for colorectal cancer, and 0.7 (95% CI, 0.4 to 1.4) for breast cancer. Corresponding hazard ratios for the highest versus the lowest quintile of baseline...

  19. Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes.

    Science.gov (United States)

    Tripathi, Charu; Mishra, Harshita; Khurana, Himani; Dwivedi, Vatsala; Kamra, Komal; Negi, Ram K; Lal, Rup

    2017-01-01

    Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C) using PacBio RSII SMRT technique. The small genome (2.01 Mbp) comprises a chromosome (1.87 Mbp) and a plasmid (143 Kbp), designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%). We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI), conserved marker genes (31 and 400), pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5) by recruiting raw metagenomic data (from the same niche) against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes. Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.

  20. Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes

    Directory of Open Access Journals (Sweden)

    Charu Tripathi

    2017-07-01

    Full Text Available Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C using PacBio RSII SMRT technique. The small genome (2.01 Mbp comprises a chromosome (1.87 Mbp and a plasmid (143 Kbp, designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%. We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI, conserved marker genes (31 and 400, pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5 by recruiting raw metagenomic data (from the same niche against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes. Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.

  1. Combined gel filtration, biuret/copper method compared with an immunochemical method for urinary protein measurement.

    Science.gov (United States)

    Peele, J D; Gadsden, R H; Loadholt, C B

    1977-01-01

    We compared an immunochemical method specific for plasma proteins with a chemical method, in which interfering substances are separated by gel filtration and "total" urinary protein is determined by the biuret reaction followed by reaction of protein-bound copper with diethyldithiocarbamate after a second gel filtration to remove nonprotein-bound copper. More than 250 24-h urine samples were analyzed by each method. There was linear agreement and a correlation of 0.96 between the two methods, but urinary protein values determined by the immunochemical method, especially for patients with multiple myeloma, were lower than by the chemical method.

  2. Multidrug Resistance-associated Protein-1 (MRP-1)-dependent Glutathione Disulfide (GSSG) Efflux as a Critical Survival Factor for Oxidant-enriched Tumorigenic Endothelial Cells.

    Science.gov (United States)

    Gordillo, Gayle M; Biswas, Ayan; Khanna, Savita; Spieldenner, James M; Pan, Xueliang; Sen, Chandan K

    2016-05-06

    Endothelial cell tumors are the most common soft tissue tumors in infants. Tumor-forming endothelial (EOMA) cells are able to escape cell death fate despite excessive nuclear oxidant burden. Our previous work recognized perinuclear Nox-4 as a key contributor to EOMA growth. The objective of this work was to characterize the mechanisms by which EOMA cells evade oxidant toxicity and thrive. In EOMA cells, compared with in the cytosol, the nuclear GSSG/GSH ratio was 5-fold higher. Compared to the ratio observed in healthy murine aortic endothelial (MAE) cells, GSSG/GSH was over twice as high in EOMA cells. Multidrug resistance-associated protein-1 (MRP-1), an active GSSG efflux mechanism, showed 2-fold increased activity in EOMA compared with MAE cells. Hyperactive YB-1 and Ape/Ref-1 were responsible for high MRP-1 expression in EOMA. Proximity ligand assay demonstrated MRP-1 and YB-1 binding. Such binding enabled the nuclear targeting of MRP-1 in EOMA in a leptomycin-B-sensitive manner. MRP-1 inhibition as well as knockdown trapped nuclear GSSG, causing cell death of EOMA. Disulfide loading of cells by inhibition of GSSG reductase (bischoloronitrosourea) or thioredoxin reductase (auranofin) was effective in causing EOMA death as well. In sum, EOMA cells survive a heavy oxidant burden by rapid efflux of GSSG, which is lethal if trapped within the cell. A hyperactive MRP-1 system for GSSG efflux acts as a critical survival factor for these cells, making it a potential target for EOMA therapeutics. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Multidrug Resistance-associated Protein-1 (MRP-1)-dependent Glutathione Disulfide (GSSG) Efflux as a Critical Survival Factor for Oxidant-enriched Tumorigenic Endothelial Cells*

    Science.gov (United States)

    Gordillo, Gayle M.; Biswas, Ayan; Khanna, Savita; Spieldenner, James M.; Pan, Xueliang; Sen, Chandan K.

    2016-01-01

    Endothelial cell tumors are the most common soft tissue tumors in infants. Tumor-forming endothelial (EOMA) cells are able to escape cell death fate despite excessive nuclear oxidant burden. Our previous work recognized perinuclear Nox-4 as a key contributor to EOMA growth. The objective of this work was to characterize the mechanisms by which EOMA cells evade oxidant toxicity and thrive. In EOMA cells, compared with in the cytosol, the nuclear GSSG/GSH ratio was 5-fold higher. Compared to the ratio observed in healthy murine aortic endothelial (MAE) cells, GSSG/GSH was over twice as high in EOMA cells. Multidrug resistance-associated protein-1 (MRP-1), an active GSSG efflux mechanism, showed 2-fold increased activity in EOMA compared with MAE cells. Hyperactive YB-1 and Ape/Ref-1 were responsible for high MRP-1 expression in EOMA. Proximity ligand assay demonstrated MRP-1 and YB-1 binding. Such binding enabled the nuclear targeting of MRP-1 in EOMA in a leptomycin-B-sensitive manner. MRP-1 inhibition as well as knockdown trapped nuclear GSSG, causing cell death of EOMA. Disulfide loading of cells by inhibition of GSSG reductase (bischoloronitrosourea) or thioredoxin reductase (auranofin) was effective in causing EOMA death as well. In sum, EOMA cells survive a heavy oxidant burden by rapid efflux of GSSG, which is lethal if trapped within the cell. A hyperactive MRP-1 system for GSSG efflux acts as a critical survival factor for these cells, making it a potential target for EOMA therapeutics. PMID:26961872

  4. The Hepatitis B Virus (HBV) HBx Protein Activates AKT To Simultaneously Regulate HBV Replication and Hepatocyte Survival

    Science.gov (United States)

    Rawat, Siddhartha

    2014-01-01

    ABSTRACT Chronic infection with hepatitis B virus (HBV) is a risk factor for developing liver diseases such as hepatocellular carcinoma (HCC). HBx is a multifunctional protein encoded by the HBV genome; HBx stimulates HBV replication and is thought to play an important role in the development of HBV-associated HCC. HBx can activate the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway in some cell lines; however, whether HBx regulates PI3K/AKT signaling in normal hepatocytes has not been evaluated. In studies described here, we assessed HBx activation of PI3K/AKT signaling in an ex vivo model of cultured primary hepatocytes and determined how this HBx activity affects HBV replication. We report that HBx activates AKT in primary hepatocytes and that the activation of AKT decreases HBV replication and HBV mRNA and core protein levels. We show that the transcription factor hepatocyte nuclear factor 4α (HNF4α) is a target of HBx-regulated AKT, and we link HNF4α to HBx-regulated AKT modulation of HBV transcription and replication. Although we and others have shown that HBx stimulates and is likely required for HBV replication, we now report that HBx also activates signals that can diminish the overall level of HBV replication. While this may seem counterintuitive, we show that an important effect of HBx activation of AKT is inhibition of apoptosis. Consequently, our studies suggest that HBx balances HBV replication and cell survival by stimulating signaling pathways that enhance hepatocyte survival at the expense of higher levels of HBV replication. IMPORTANCE Chronic hepatitis B virus (HBV) infection is a common cause of the development of liver cancer. Regulation of cell signaling pathways by the HBV HBx protein is thought to influence the development of HBV-associated liver cancer. HBx stimulates, and may be essential for, HBV replication. We show that HBx activates AKT in hepatocytes to reduce HBV replication. While this seems contradictory to an

  5. Survival of patients with Stage III colon cancer is improved in hereditary non-polyposis colorectal cancer compared with sporadic cases. A Danish registry based study.

    Science.gov (United States)

    Brixen, L M; Bernstein, I T; Bülow, S; Ehrnrooth, E

    2013-07-01

    Patients with hereditary non-polyposis colorectal cancer (HNPCC) seem to have a better prognosis than those with sporadic colorectal cancer (CRC). The aim was to compare survival after Stage III CC in patients with HNPCC with those having sporadic CC. A total of 230 patients with hereditary cancer from the Danish HNPCC Register and 3557 patients with sporadic CC from the Danish Colorectal Cancer Database, diagnosed during May 2001-December 2008, were included. HNPCC patients were classified according to mismatch repair mutation status and family pedigree. Sporadic cases had no known family history of cancer. Patient characteristics, geographical differences and survival data were analysed. The overall survival (OS) was better in HNPCC patients compared with sporadic CC after stratification for sex and age (P = 0.02; CI 1.04-1.7). The 5-year survival was 70% in HNPCC patients compared with 56% in sporadic CC (P < 0.001). No survival difference was found between HNPCC subgroups but a tendency to better OS was seen in patients with Lynch syndrome. No geographical differences in OS were found. The median follow-up was 3.9 (0-9.5) years for HNPCC vs 3.2 (0-9.6) years for sporadic CC. HNPCC patients with Stage III CC have a better OS compared with sporadic CC. No significant difference in OS was found within HNPCC subgroups. Colorectal Disease © 2013 The Association of Coloproctology of Great Britain and Ireland.

  6. Investigation of glandular trichome proteins in Artemisia annua L. using comparative proteomics.

    Directory of Open Access Journals (Sweden)

    Ting Wu

    Full Text Available Glandular secreting trichomes (GSTs are called biofactories because they are active in synthesizing, storing and secreting various types of plant secondary metabolites. As the most effective drug against malaria, artemisinin, a sesquiterpene lactone is derived from GSTs of Artemisia annua. However, low artemisinin content (0.001%~1.54% of dry weight has hindered its wide application. We investigate the GST-expressed proteins in Artemisia annua using a comparative proteomics approach, aiming for a better understanding of the trichome proteome and arteminisin metabolism. 2D-electrophoresis was employed to compare the protein profiles of GSTs and leaves. More than 700 spots were resolved for GSTs, of which ∼93 non-redundant proteins were confidently identified by searching NCBI and Artemisia EST databases. Over 70% of these proteins were highly expressed in GTSs. Functional classification of these GSTs enriched proteins revealed that many of them participate in major plant metabolic processes such as electron transport, transcription and translation.

  7. [Long term biochemical recurrence free survival after radical prostatectomy for cancer: comparative analysis according to surgical approach and clinicopathological stage].

    Science.gov (United States)

    Rizk, J; Ouzzane, A; Flamand, V; Fantoni, J-C; Puech, P; Leroy, X; Villers, A

    2015-03-01

    To assess long term biochemical recurrence free survival after radical prostatectomy according to open, laparoscopic and robot-assisted surgical approach and clinicopathological stage. A cohort study of 1313 consecutive patients treated by radical prostatectomy for localized or locally advanced prostate cancer between 2000 and 2013. Open surgery (63.7%), laparoscopy (10%) and robot-assisted laparoscopy (26.4%) were performed. Biochemical recurrence was defined by PSA>0,1ng/mL. The biochemical recurrence free survival was described by Kaplan Meier method and prognostic factors were analysed by multivariable Cox regression. Median follow-up was 57 months (IQR: 31-90). Ten years biochemical recurrence free survival was 88.5%, 71.6% and 53.5% respectively for low, intermediate and high-risk D'Amico groups. On multivariable analysis, the worse prognostic factor was Gleason score (PBiochemical recurrence free survival (P=0.06) and positive surgical margins rate (P=0.87) were not statistically different between the three surgical approaches. Biochemical recurrence free survival in our study does not differ according to surgical approach and is similar to published series. Ten years biochemical recurrence free survival for high-risk tumours without hormone therapy is 54% justifying the role of surgery in the therapeutic conversations in this group of tumours. 3. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  8. Squamous Cancers of the Rectum Demonstrate Poorer Survival and Increased Need for Salvage Surgery Compared With Squamous Cancers of the Anus.

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    Kulaylat, Audrey S; Hollenbeak, Christopher S; Stewart, David B

    2017-09-01

    Squamous cell cancers of the anus are rare GI malignancies for which neoadjuvant chemoradiation is the first-line treatment for nonmetastatic disease. Squamous cancers of the rectum are far less common, and it is unclear to what degree chemoradiotherapy improves their outcomes. The purpose of this study was to compare stage-specific survival for anal and rectal squamous cancers stratified by treatment approach. This was a retrospective cohort study. The study was conducted at Commission on Cancer designated hospitals. Patients (2006-2012) identified in the National Cancer Database with pretreatment clinical stage I to III cancers who underwent chemoradiotherapy, with and without subsequent salvage surgical resection (low anterior resection or abdominoperineal resection), ≥12 weeks after chemoradiotherapy were included in the study. Overall survival and the need for salvage surgery were measured. Anal cancers (n = 11,224) typically presented with stage II (45.7%) or III (36.3%) disease, whereas rectal cancer stages (n = 1049) were more evenly distributed (p cancer underwent low anterior or abdominoperineal resections 12 weeks or later after chemoradiotherapy versus those undergoing abdominoperineal resection for anal cancer (3.8% versus 1.2%; p cancer was associated with poorer survival compared with anal cancer (stage I, p = 0.017; stage II, p cancer was associated with worse survival for stage I to III cancers; salvage surgery did not significantly affect survival for rectal cancer. This was a retrospective study without cancer-specific survival measures. Squamous rectal cancers are associated with significantly worse survival than squamous cancers of the anus for clinical stage I and II disease. Despite both cancers exhibiting squamous histology, rectal cancers may be less radiosensitive than anal cancers, as suggested by the greater incidence of salvage surgery that does not appear to significantly improve overall survival. See Video Abstract at http

  9. Classic Ras Proteins Promote Proliferation and Survival Via Distinct Phosphoproteome Alterations in Neurofibromin-Null Malignant Peripheral Nerve Sheath Tumor Cells

    Science.gov (United States)

    Brossier, Nicole M.; Prechtl, Amanda M.; Longo, Jody Fromm; Barnes, Stephen; Wilson, Landon S.; Byer, Stephanie J.; Brosius, Stephanie N.; Carroll, Steven L.

    2015-01-01

    Neurofibromin, the tumor suppressor encoded by the neurofibromatosis type 1 (NF1) gene, potentially suppresses the activation of H-Ras, N-Ras and K-Ras. However, it is not known whether these classic Ras proteins are hyperactivated in NF1-null nerve sheath tumors, how they contribute to tumorigenesis and what signaling pathways mediate their effects. Here we show that H-Ras, N-Ras and K-Ras are coexpressed with their activators, (guanine nucleotide exchange factors), in neurofibromin-null malignant peripheral nerve sheath tumor (MPNST) cells and that all 3 Ras proteins are activated. Dominant negative (DN) H-Ras, a pan-inhibitor of the classic Ras family, inhibited MPNST proliferation and survival, but not migration. However, NF1-null MPNST cells were variably dependent on individual Ras proteins. In some lines, ablation of H-Ras, N-Ras and/or K-Ras inhibited mitogenesis. In others, ablation of a single Ras protein had no effect on proliferation; in these lines, ablation of a single Ras protein resulted in compensatory increases in the activation and/or expression of other Ras proteins. Using mass spectrometry-based phosphoproteomics, we identified 7 signaling networks affecting morphology, proliferation and survival that are regulated by DN H-Ras. Thus, neurofibromin loss activates multiple classic Ras proteins that promote proliferation and survival by regulating several distinct signaling cascades. PMID:25946318

  10. NTCP modelling of lung toxicity after SBRT comparing the universal survival curve and the linear quadratic model for fractionation correction.

    Science.gov (United States)

    Wennberg, Berit M; Baumann, Pia; Gagliardi, Giovanna; Nyman, Jan; Drugge, Ninni; Hoyer, Morten; Traberg, Anders; Nilsson, Kristina; Morhed, Elisabeth; Ekberg, Lars; Wittgren, Lena; Lund, Jo-Åsmund; Levin, Nina; Sederholm, Christer; Lewensohn, Rolf; Lax, Ingmar

    2011-05-01

    In SBRT of lung tumours no established relationship between dose-volume parameters and the incidence of lung toxicity is found. The aim of this study is to compare the LQ model and the universal survival curve (USC) to calculate biologically equivalent doses in SBRT to see if this will improve knowledge on this relationship. Toxicity data on radiation pneumonitis grade 2 or more (RP2+) from 57 patients were used, 10.5% were diagnosed with RP2+. The lung DVHs were corrected for fractionation (LQ and USC) and analysed with the Lyman- Kutcher-Burman (LKB) model. In the LQ-correction α/β = 3 Gy was used and the USC parameters used were: α/β = 3 Gy, D(0) = 1.0 Gy, [Formula: see text] = 10, α = 0.206 Gy(-1) and d(T) = 5.8 Gy. In order to understand the relative contribution of different dose levels to the calculated NTCP the concept of fractional NTCP was used. This might give an insight to the questions of whether "high doses to small volumes" or "low doses to large volumes" are most important for lung toxicity. NTCP analysis with the LKB-model using parameters m = 0.4, D(50) = 30 Gy resulted for the volume dependence parameter (n) with LQ correction n = 0.87 and with USC correction n = 0.71. Using parameters m = 0.3, D(50) = 20 Gy n = 0.93 with LQ correction and n = 0.83 with USC correction. In SBRT of lung tumours, NTCP modelling of lung toxicity comparing models (LQ,USC) for fractionation correction, shows that low dose contribute less and high dose more to the NTCP when using the USC-model. Comparing NTCP modelling of SBRT data and data from breast cancer, lung cancer and whole lung irradiation implies that the response of the lung is treatment specific. More data are however needed in order to have a more reliable modelling.

  11. Comparative analysis of human reproductive proteomes identifies candidate proteins of sperm maturation.

    Science.gov (United States)

    Fu-Jun, Liu; Xiao-Fang, Shen

    2012-12-01

    Male reproductive proteomes provide basis for studying gene products and its involvement or regulation in sperm physiology. Here, a comparative study between these proteomes was performed to find potential proteins and functions associated with human sperm maturation. Seven reproductive proteomes associated with human sperm physiology were integrated. Gene ontology analysis were performed using DAVID and Panther tools to determine enriched functions. Total of 270 proteins overlapped between epididymal, prostatic milieu and sperm proteome were thought to be candidate proteins involved in sperm maturation, and they showed enriched functions of proteasomal protein catabolic process and protein folding. 34 epididymal milieu proteins and 274 prostatic milieu proteins were contributed to the composition of seminal fluids proteome. Literatures have confirmed the involvements in sperm maturation of many of these proteins The spatial expressions of 24 epididymal milieu proteins involved in chaperone and antioxidant activity were authenticated by real-time RT-PCR. These proteins may serve as candidate molecules for future studies of sperm maturation and male infertility.

  12. Comparative modelling of protein structure and its impact on microbial cell factories

    Directory of Open Access Journals (Sweden)

    Oliva Baldomero

    2005-06-01

    Full Text Available Abstract Comparative modeling is becoming an increasingly helpful technique in microbial cell factories as the knowledge of the three-dimensional structure of a protein would be an invaluable aid to solve problems on protein production. For this reason, an introduction to comparative modeling is presented, with special emphasis on the basic concepts, opportunities and challenges of protein structure prediction. This review is intended to serve as a guide for the biologist who has no special expertise and who is not involved in the determination of protein structure. Selected applications of comparative modeling in microbial cell factories are outlined, and the role of microbial cell factories in the structural genomics initiative is discussed.

  13. Apelin Compared With Dobutamine Exerts Cardioprotection and Extends Survival in a Rat Model of Endotoxin-Induced Myocardial Dysfunction.

    Science.gov (United States)

    Chagnon, Frederic; Coquerel, David; Salvail, Dany; Marsault, Eric; Dumaine, Robert; Auger-Messier, Mannix; Sarret, Philippe; Lesur, Olivier

    2017-04-01

    Dobutamine is the currently recommended β-adrenergic inotropic drug for supporting sepsis-induced myocardial dysfunction when cardiac output index remains low after preload correction. Better and safer therapies are nonetheless mandatory because responsiveness to dobutamine is limited with numerous side effects. Apelin-13 is a powerful inotropic candidate that could be considered as an alternative noncatecholaminergic support in the setting of inflammatory cardiovascular dysfunction. Interventional controlled experimental animal study. Tertiary care university-based research institute. One hundred ninety-eight adult male rats. Using a rat model of "systemic inflammation-induced cardiac dysfunction" induced by intraperitoneal lipopolysaccharide injection (10 mg/kg), hemodynamic efficacy, cardioprotection, and biomechanics were assessed under IV osmotic pump infusions of apelin-13 (0.25 μg/kg/min) or dobutamine (7.5 μg/kg/min). In this model and in both in vivo and ex vivo studies, apelin-13 compared with dobutamine provoked distinctive effects on cardiac function: 1) optimized cardiac energy-dependent workload with improved cardiac index and lower vascular resistance, 2) upgraded hearts' apelinergic responsiveness, and 3) consecutive downstream advantages, including increased urine output, enhanced plasma volume, reduced weight loss, and substantially improved overall outcomes. In vitro studies confirmed that these apelin-13-driven processes encompassed a significant and rapid reduction in systemic cytokine release with dampening of myocardial inflammation, injury, and apoptosis and resolution of associated molecular pathways. In this inflammatory cardiovascular dysfunction, apelin-13 infusion delivers distinct and optimized hemodynamic support (including positive fluid balance), along with cardioprotective effects, modulation of circulatory inflammation and extended survival.

  14. Regulator of G-Protein Signaling 5 Reduces HeyA8 Ovarian Cancer Cell Proliferation and Extends Survival in a Murine Tumor Model

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    Molly K. Altman

    2012-01-01

    Full Text Available The regulator of G-protein signaling 5 (RGS5 belongs to a family of GTPase activators that terminate signaling cascades initiated by extracellular mediators and G-protein-coupled receptors. RGS5 has an interesting dual biological role. One functional RGS5 role is as a pericyte biomarker influencing the switch to angiogenesis during malignant progression. Its other functional role is to promote apoptosis in hypoxic environments. We set out to clarify the extent to which RGS5 expression regulates tumor progression—whether it plays a pathogenic or protective role in ovarian tumor biology. We thus constructed an inducible gene expression system to achieve RGS5 expression in HeyA8-MDR ovarian cancer cells. Through this we observed that inducible RGS5 expression significantly reduces in vitro BrdU-positive HeyA8-MDR cells, although this did not correlate with a reduction in tumor volume observed using an in vivo mouse model of ovarian cancer. Interestingly, mice bearing RGS5-expressing tumors demonstrated an increase in survival compared with controls, which might be attributed to the vast regions of necrosis observed by pathological examination. Additionally, mice bearing RGS5-expressing tumors were less likely to have ulcerated tumors. Taken together, this data supports the idea that temporal expression and stabilization of RGS5 could be a valuable tactic within the context of a multicomponent approach for modulating tumor progression.

  15. Neoadjuvant chemotherapy is associated with improved survival compared with adjuvant chemotherapy in patients with triple-negative breast cancer only after complete pathologic response.

    Science.gov (United States)

    Fisher, Carla S; Ma, Cynthia X; Gillanders, William E; Aft, Rebecca L; Eberlein, Timothy J; Gao, Feng; Margenthaler, Julie A

    2012-01-01

    Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer that is known to be chemosensitive. In patients with TNBC, we sought to compare survival outcomes between patients receiving neoadjuvant chemotherapy, with and without complete pathologic response (pCR), and those receiving adjuvant chemotherapy. We performed a retrospective chart review and identified 385 patients with stage I-III TNBC who were treated with neoadjuvant or adjuvant chemotherapy between 2000 and 2008. Patients were divided according to receipt of neoadjuvant chemotherapy with pCR, neoadjuvant chemotherapy without pCR, and adjuvant chemotherapy. Data were compared using Fisher's exact test and analysis of variance (ANOVA). Kaplan-Meier curves were generated. Of 385 patients, 151 (39%) received neoadjuvant chemotherapy and 234 (61%) received adjuvant chemotherapy. Twenty-six (17%) of those patients receiving neoadjuvant chemotherapy had pCR. After controlling for covariates associated with survival in unadjusted tests, patients undergoing neoadjuvant chemotherapy with residual tumor had significantly worse survival compared with patients receiving adjuvant therapy [hazard ratio (HR) = 0.51, P = 0.007] and a trend towards worse survival compared with patients receiving neoadjuvant therapy with pCR (HR = 0.19, P = 0.10). Although previous clinical trials have not demonstrated a survival difference between patients receiving neoadjuvant versus adjuvant chemotherapy for breast cancer, our study suggests an overall survival benefit in patients with pCR following neoadjuvant chemotherapy compared with patients receiving adjuvant therapy. It is clear that a prospective study needs to be carried out to better elucidate the timing of chemotherapy in patients with TNBC.

  16. Reduced-intensity allogeneic hematopoietic stem cell transplantation combined with imatinib has comparable event-free survival and overall survival to long-term imatinib treatment in young patients with chronic myeloid leukemia.

    Science.gov (United States)

    Zhao, Yanmin; Wang, Jiasheng; Luo, Yi; Shi, Jimin; Zheng, Weiyan; Tan, Yamin; Cai, Zhen; Huang, He

    2017-08-01

    The relative merits of reduced intensity hematopoietic stem cell transplantation (RIST) for chronic myeloid leukemia (CML) in the first chronic phase (CP) in imatinib era have not been evaluated. The study was designed to compare the outcomes of combination therapy of RIST plus imatinib (RIST + IM) vs. imatinib (IM) alone for young patients with early CP (ECP) and late CP (LCP). Of the patients, 130 were non-randomly assigned to treatment with IM alone (n = 88) or RIST + IM (n = 42). The 10-year overall survival (OS) and event-free survival (EFS) were comparable between RIST + IM and IM groups. LCP, high Sokal score, and no complete cytogenetic response at 3 months were adverse prognostic factors for survival, but only the time from diagnosis to IM was an independent predictor after multivariate analysis. For ECP, IM was similar to RIST + IM, with 10-year EFS rates of 77.2 vs. 81.6% (p = 0.876) and OS rates of 93.8 vs. 87.9% (p = 0.102), respectively. For LCP, both treatments resulted in similar survival, but more patients in the imatinib group experienced events (10-year EFS 40.8 vs. 66.7%, p = 0.047). The patients with higher EBMT risk scores had an inferior survival than those with lower scores (69.2 vs. 92.9%, p = 0.04). We concluded that RIST + IM was comparable to IM in terms of OS and EFS. However, RIST + IM was more affordable than IM alone in a 10-year scale. Thus, RIST + IM could be considered as an alternative treatment option, especially when the patients have low EBMT risk scores and demand a definite cure for CML.

  17. ID helix-loop-helix proteins as determinants of cell survival in B-cell chronic lymphocytic leukemia cells in vitro.

    Science.gov (United States)

    Weiler, Sarah; Ademokun, Jolaolu A; Norton, John D

    2015-02-03

    Members of the inhibitor of DNA-binding (ID) family of helix-loop-helix proteins have been causally implicated in the pathogenesis of several types of B-cell lineage malignancy, either on the basis of mutation or by altered expression. B-cell chronic lymphocytic leukemia encompasses a heterogeneous group of disorders and is the commonest leukaemia type in the Western world. In this study, we have investigated the pathobiological functions of the ID2 and ID3 proteins in this disease with an emphasis on their role in regulating leukemic cell death/survival. Bioinformatics analysis of microarray gene expression data was used to investigate expression of ID2/ID3 in leukemic versus normal B cells, their association with clinical course of disease and molecular sub-type and to reconstruct a gene regulatory network using the 'maximum information coefficient' (MIC) for target gene inference. In vitro cultured primary leukemia cells, either in isolation or co-cultured with accessory vascular endothelial cells, were used to investigate ID2/ID3 protein expression by western blotting and to assess the cytotoxic response of different drugs (fludarabine, chlorambucil, ethacrynic acid) by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. ID2/ID3 protein levels in primary leukemia cells and in MEC1 cells were manipulated by transduction with siRNA reagents. Datamining showed that the expression profiles of ID2 and ID3 are associated with distinct pathobiological features of disease and implicated both genes in regulating cell death/survival by targeting multiple non-overlapping sets of apoptosis effecter genes. Consistent with microarray data, the overall pattern of ID2/ID3 protein expression in relation to cell death/survival responses of primary leukemia cells was suggestive of a pro-survival function for both ID proteins. This was confirmed by siRNA knock-down experiments in MEC1 cells and in primary leukemia cells, but with variability in the dependence of

  18. Modulation of Trehalose Dimycolate and Immune System by Rv0774c Protein Enhanced the Intracellular Survival of Mycobacterium smegmatis in Human Macrophages Cell Line

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    Arbind Kumar

    2017-06-01

    Full Text Available Mycobacterium tuberculosis Rv0774c protein was reported previously to express under stress conditions. Therefore, Rv0774c gene was cloned and expressed in Mycobacterium smegmatis, a surrogate host, to determine its role in bacterial persistence and immune modulation in natural environment. The bacterial colonies expressing Rv0774c (Ms_rv0774c were larger, smoother, more moist, and flatter than the control ones (Ms_ve. Enhanced survival of Ms_rv0774c after treatment with streptomycin was observed when compared with control. The cell envelope of Ms_rv0774c was demonstrated to have more trehalose di-mycolate (TDM and lesser amount of mycolylmannosylphosphorylheptaprenol (Myc-PL in comparison to control. Higher intracellular survival rate was observed for Ms_rv0774c as compared to Ms_ve in the THP-1 cells. This could be correlated to the reduction in the levels of reactive NO and iNOS expression. Infection of macrophages with Ms_rv0774c resulted in significantly increased expression of TLR2 receptor and IL-10 cytokines. However, it lowered the production of pro-inflammatory cytokines such as IL-12, TNF-α, IFN-γ, and MCP-1 in Ms_rv0774c infected macrophages in comparison to the control and could be associated with decreased phosphorylation of p38 MAPK. Though, predicted with high antigenicity index bioinformatically, extracellular in nature and accessible to host milieu, Rv0774c was not able to generate humoral response in patient samples. Overall, the present findings indicated that Rv0774c altered the morphology and streptomycin sensitivity by altering the lipid composition of M. smegmatis as well as modulated the immune response in favor of bacterial persistence.

  19. Expression of freeze-responsive proteins, Fr10 and Li16, from freeze-tolerant frogs enhances freezing survival of BmN insect cells.

    Science.gov (United States)

    Biggar, Kyle K; Kotani, Eiji; Furusawa, Toshiharu; Storey, Kenneth B

    2013-08-01

    To date, two novel freeze-responsive proteins, Fr10 and Li16, have been discovered in the wood frog, Rana sylvatica, and likely support freezing survival. Although previous studies have established tissue distribution of each protein, there have been no studies that explore their functional consequences in intolerant cells. To assess the ability of Fr10 and Li16 to confer freeze tolerance, we transfected each protein into a freeze-intolerant silkworm cell line (BmN). Selected controls were the transfection of an unrelated protein (CAT) and a no-transfection sample. Li16 and Fr10 showed 1.8 ± 0.1- and 1.7 ± 0.2-fold, respectively, greater survival after freezing at -6°C for 1 h than did transfection controls. To investigate how these novel proteins protect cells from freezing damage, protein structures were predicted from primary amino acid sequences. Analysis of the structures indicated that Fr10 is a secreted protein and may be a new type IV antifreeze protein, whereas Li16 may have intracellular membrane associated functions. This study shows that freezing protection can be provided to intolerant cells by the overexpression of transfected Li16 and Fr10 frog proteins. Results from this study will provide new insights into adapting intolerant cells for medical organ cryoprotection using a natural vertebrate model of tolerance.

  20. Comparative proteomics of milk fat globule membrane proteins from transgenic cloned cattle.

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    Shunchao Sui

    Full Text Available The use of transgenic livestock is providing new methods for obtaining pharmaceutically useful proteins. However, the protein expression profiles of the transgenic animals, including expression of milk fat globule membrane (MFGM proteins, have not been well characterized. In this study, we compared the MFGM protein expression profile of the colostrum and mature milk from three lines of transgenic cloned (TC cattle, i.e., expressing recombinant human α-lactalbumin (TC-LA, lactoferrin (TC-LF or lysozyme (TC-LZ in the mammary gland, with those from cloned non-transgenic (C and conventionally bred normal animals (N. We identified 1, 225 proteins in milk MFGM, 166 of which were specifically expressed only in the TC-LA group, 265 only in the TC-LF group, and 184 only in the TC-LZ group. There were 43 proteins expressed only in the transgenic cloned animals, but the concentrations of these proteins were below the detection limit of silver staining. Functional analysis also showed that the 43 proteins had no obvious influence on the bovine mammary gland. Quantitative comparison revealed that MFGM proteins were up- or down-regulated more than twofold in the TC and C groups compared to N group: 126 in colostrum and 77 in mature milk of the TC-LA group; 157 in colostrum and 222 in mature milk of the TC-LF group; 49 in colostrum and 98 in mature milk of the TC-LZ group; 98 in colostrum and 132 in mature milk in the C group. These up- and down-regulated proteins in the transgenic animals were not associated with a particular biological function or pathway, which appears that expression of certain exogenous proteins has no general deleterious effects on the cattle mammary gland.

  1. Convergent RANK- and c-Met-mediated signaling components predict survival of patients with prostate cancer: an interracial comparative study.

    Science.gov (United States)

    Hu, Peizhen; Chung, Leland W K; Berel, Dror; Frierson, Henry F; Yang, Hua; Liu, Chunyan; Wang, Ruoxiang; Li, Qinlong; Rogatko, Andre; Zhau, Haiyen E

    2013-01-01

    We reported (PLoS One 6 (12):e28670, 2011) that the activation of c-Met signaling in RANKL-overexpressing bone metastatic LNCaP cell and xenograft models increased expression of RANK, RANKL, c-Met, and phosphorylated c-Met, and mediated downstream signaling. We confirmed the significance of the RANK-mediated signaling network in castration resistant clinical human prostate cancer (PC) tissues. In this report, we used a multispectral quantum dot labeling technique to label six RANK and c-Met convergent signaling pathway mediators simultaneously in formalin fixed paraffin embedded (FFPE) tissue specimens, quantify the intensity of each expression at the sub-cellular level, and investigated their potential utility as predictors of patient survival in Caucasian-American, African-American and Chinese men. We found that RANKL and neuropilin-1 (NRP-1) expression predicts survival of Caucasian-Americans with PC. A Gleason score ≥ 8 combined with nuclear p-c-Met expression predicts survival in African-American PC patients. Neuropilin-1, p-NF-κB p65 and VEGF are predictors for the overall survival of Chinese men with PC. These results collectively support interracial differences in cell signaling networks that can predict the survival of PC patients.

  2. Convergent RANK- and c-Met-mediated signaling components predict survival of patients with prostate cancer: an interracial comparative study.

    Directory of Open Access Journals (Sweden)

    Peizhen Hu

    Full Text Available We reported (PLoS One 6 (12:e28670, 2011 that the activation of c-Met signaling in RANKL-overexpressing bone metastatic LNCaP cell and xenograft models increased expression of RANK, RANKL, c-Met, and phosphorylated c-Met, and mediated downstream signaling. We confirmed the significance of the RANK-mediated signaling network in castration resistant clinical human prostate cancer (PC tissues. In this report, we used a multispectral quantum dot labeling technique to label six RANK and c-Met convergent signaling pathway mediators simultaneously in formalin fixed paraffin embedded (FFPE tissue specimens, quantify the intensity of each expression at the sub-cellular level, and investigated their potential utility as predictors of patient survival in Caucasian-American, African-American and Chinese men. We found that RANKL and neuropilin-1 (NRP-1 expression predicts survival of Caucasian-Americans with PC. A Gleason score ≥ 8 combined with nuclear p-c-Met expression predicts survival in African-American PC patients. Neuropilin-1, p-NF-κB p65 and VEGF are predictors for the overall survival of Chinese men with PC. These results collectively support interracial differences in cell signaling networks that can predict the survival of PC patients.

  3. Survival advantage from ventricular fibrillation and pulseless electrical activity in women compared to men: the Oregon Sudden Unexpected Death Study.

    Science.gov (United States)

    Teodorescu, Carmen; Reinier, Kyndaron; Uy-Evanado, Audrey; Ayala, Jo; Mariani, Ronald; Wittwer, Lynn; Gunson, Karen; Jui, Jonathan; Chugh, Sumeet S

    2012-09-01

    Studies evaluating a possible survival advantage from sudden cardiac arrest (SCA) in women have produced mixed results possibly due to a lack of comprehensive analyses. We hypothesized that race, socioeconomic status (SES), and elements of the lifetime clinical history influence gender effects and need to be incorporated within analyses of survival. Cases of SCA were identified from the ongoing, prospective, multiple-source Oregon Sudden Unexpected Death Study (population approximately one million). Subjects included were age ≥18 years who underwent attempted resuscitation by EMS providers. Pearson's chi-square tests and independent samples t tests or analysis of variance were used for univariate comparisons. We evaluated gender and race differences in survival adjusted for age, circumstances of arrest, disease burden, and socioeconomic status using a logistic regression model predicting survival. A total of 1,296 cases had resuscitation attempted (2002-2007; mean age 65 years, male 67%). Women were older than men (68 vs. 63 years, p ratio 1.85; 95% confidence interval (1.12-3.04)]. Despite older age, higher prevalence of SCA in the home, and higher rates of PEA, women had a survival advantage from ventricular fibrillation and pulseless electrical activity.

  4. A Basic Protein Comparative Three-Dimensional Modeling Methodological Workflow Theory and Practice.

    Science.gov (United States)

    Bitar, Mainá; Franco, Glória Regina

    2014-01-01

    When working with proteins and studying its properties, it is crucial to have access to the three-dimensional structure of the molecule. If experimentally solved structures are not available, comparative modeling techniques can be used to generate useful protein models to subsidize structure-based research projects. In recent years, with Bioinformatics becoming the basis for the study of protein structures, there is a crescent need for the exposure of details about the algorithms behind the softwares and servers, as well as a need for protocols to guide in silico predictive experiments. In this article, we explore different steps of the comparative modeling technique, such as template identification, sequence alignment, generation of candidate structures and quality assessment, its peculiarities and theoretical description. We then present a practical step-by-step workflow, to support the Biologist on the in silico generation of protein structures. Finally, we explore further steps on comparative modeling, presenting perspectives to the study of protein structures through Bioinformatics. We trust that this is a thorough guide for beginners that wish to work on the comparative modeling of proteins.

  5. Muscle A-Kinase Anchoring Protein-α is an Injury-Specific Signaling Scaffold Required for Neurotrophic- and Cyclic Adenosine Monophosphate-Mediated Survival

    Directory of Open Access Journals (Sweden)

    Yan Wang

    2015-12-01

    Full Text Available Neurotrophic factor and cAMP-dependent signaling promote the survival and neurite outgrowth of retinal ganglion cells (RGCs after injury. However, the mechanisms conferring neuroprotection and neuroregeneration downstream to these signals are unclear. We now reveal that the scaffold protein muscle A-kinase anchoring protein-α (mAKAPα is required for the survival and axon growth of cultured primary RGCs. Although genetic deletion of mAKAPα early in prenatal RGC development did not affect RGC survival into adulthood, nor promoted the death of RGCs in the uninjured adult retina, loss of mAKAPα in the adult increased RGC death after optic nerve crush. Importantly, mAKAPα was required for the neuroprotective effects of brain-derived neurotrophic factor and cyclic adenosine-monophosphate (cAMP after injury. These results identify mAKAPα as a scaffold for signaling in the stressed neuron that is required for RGC neuroprotection after optic nerve injury.

  6. Synthesis of a designed transmembrane protein by thioether ligation of solubilised segments : Nα-haloacetylated peptides survived resin cleavage using TFA with EDT as scavenger

    NARCIS (Netherlands)

    Englebretsen, D.R; Choma, C.T.; Robillard, G.T.

    1998-01-01

    Nα-haloacetylated peptides made by Fmoc solid phase synthesis survived cleavage when EDT was used as a cleavage component. Two segments of a desgned transmembrane protein, one bromoacetylated, the other containing a cysteine, and each bearing a "solubilising tail" peptide, were synthesised by Fmoc

  7. COMPARATIVE MODELLING PROTEIN VAKSIN NA BTB H5N1 MENGGUNAKAN SWISS MODEL

    Directory of Open Access Journals (Sweden)

    Fitri Amelia

    2016-09-01

    Full Text Available Vaccine sequence of Neuraminidase BTB from previous research was studied by using swiss model server. Protein template was gotten from RSCB database by comparing the vaccine sequence with PDB database. HTY protein was used as a template for this vaccine. Template had 0.00e-1 E value, and 97% identity. The protein vaccine that has been modelled by swiss model had  good quality as immune inducer. Base on ramachandran plot analysis, protein model 1, 2, and 3 have amino acid residues in favoured region higher than 70%. They are 82,0% and 78,2%. Model 1 has the lowest non glysine amino acid residues in disallowed region area, that is 0%.   3D Structure of vaccine had 2086  hits of similarity with database on NCBI   Key words: comparing modelling, H5N1 vaccine, swiss model

  8. A comparative study of generalized linear mixed modelling and artificial neural network approach for the joint modelling of survival and incidence of Dengue patients in Sri Lanka

    Science.gov (United States)

    Hapugoda, J. C.; Sooriyarachchi, M. R.

    2017-09-01

    Survival time of patients with a disease and the incidence of that particular disease (count) is frequently observed in medical studies with the data of a clustered nature. In many cases, though, the survival times and the count can be correlated in a way that, diseases that occur rarely could have shorter survival times or vice versa. Due to this fact, joint modelling of these two variables will provide interesting and certainly improved results than modelling these separately. Authors have previously proposed a methodology using Generalized Linear Mixed Models (GLMM) by joining the Discrete Time Hazard model with the Poisson Regression model to jointly model survival and count model. As Aritificial Neural Network (ANN) has become a most powerful computational tool to model complex non-linear systems, it was proposed to develop a new joint model of survival and count of Dengue patients of Sri Lanka by using that approach. Thus, the objective of this study is to develop a model using ANN approach and compare the results with the previously developed GLMM model. As the response variables are continuous in nature, Generalized Regression Neural Network (GRNN) approach was adopted to model the data. To compare the model fit, measures such as root mean square error (RMSE), absolute mean error (AME) and correlation coefficient (R) were used. The measures indicate the GRNN model fits the data better than the GLMM model.

  9. Characterization of the comparative drug binding to intra- (liver fatty acid binding protein) and extra- (human serum albumin) cellular proteins.

    Science.gov (United States)

    Rowland, Andrew; Hallifax, David; Nussio, Matthew R; Shapter, Joseph G; Mackenzie, Peter I; Brian Houston, J; Knights, Kathleen M; Miners, John O

    2015-01-01

    1. This study compared the extent, affinity, and kinetics of drug binding to human serum albumin (HSA) and liver fatty acid binding protein (LFABP) using ultrafiltration and surface plasmon resonance (SPR). 2. Binding of basic and neutral drugs to both HSA and LFABP was typically negligible. Binding of acidic drugs ranged from minor (fu > 0.8) to extensive (fu transport mechanisms for drugs bound moderately or extensively to HSA and LFABP.

  10. Inferior survival for young patients with contralateral compared to unilateral breast cancer : A nationwide population-based study in the Netherlands

    NARCIS (Netherlands)

    Font-Gonzalez, A.; Liu, L.; Voogd, A.C.; Schmidt, M.; Roukema, J.A.; Coebergh, J.W.; de Vries, E.; Soerjomataram, I.

    To compare overall survival between women with unilateral breast cancer (UBC) and contralateral breast cancer (CBC). Women with UBC (N = 182,562; 95 %) and CBC (N = 8,912; 5 %) recorded in the Netherlands Cancer Registry between 1989 and 2008 were included and followed until 2010. We incorporated

  11. Growth, feed utilization, survival and body composition of fingerlings of Slender walking catfish, Clarias nieuhofii, fed diets containing different protein levels

    Directory of Open Access Journals (Sweden)

    Anut Kiriratnikom

    2012-02-01

    Full Text Available The effects of test diets, containing different dietary protein levels (32, 36, 40, and 44%, on growth, feed conversionrate and survival of slender walking catfish (Clarias nieuhofii fingerlings were studied. Fish with an average weight of8.35-8.46 g were fed with isocaloric test diets containing 32, 36, 40 and 44% protein, for 12 weeks. The average body weightof the fish fed 40% - 44% protein was significantly higher than that of the others within 4 weeks of feeding (P<0.05. Attermination of the experiment, average body weight and weight gain of the fish fed the diet containing 40% and 44% proteinwere highest and were significantly different from those of the fish fed 32% to 36% protein (P<0.05. The lowest feed conversionrate (FCR was observed in the fish fed 40% and 44% protein. Condition factors (CF were lowest in the fish thatreceived 32% and 36% protein test diets, and hepatosomatic indices (HSI were increased by the dietary protein levels butwere not significantly different in the fish fed protein in the range of 36% to 44%. Carcass composition analysis indicated apositive correlation between dietary protein level and fish body protein content, but moisture, lipid level and ash content inthe fish body were not significantly different among treatments. In conclusion, the 40% protein diet gave the maximumgrowth performance, lowest feed conversion ratio and high body protein content in slender walking catfish fingerling duringthe 12 weeks of the feeding trial.

  12. Comparative survival of Escherichia coli O157:H7, Salmonella Typhimurium, and Murine Norovirus on spinach plants

    Science.gov (United States)

    Introduction: Outbreaks resulting from the consumption of leafy greens contaminated with E. coli O157:H7, Salmonella spp., and norovirus have occurred. It is unclear how the stress response factor rpoS in E. coli O157:H7 and Salmonella spp. affects their survival on spinach. Purpose: A comparison ...

  13. Comparative off-host survival of larval Rocky Mountain Wood Ticks (Dermacentor andersoni) collected from ecologically distinct field populations.

    Science.gov (United States)

    Owen, J P; Vander Vliet, A; Scoles, G A

    2014-09-01

    Dermacentor andersoni (Ixodida: Ixodidae) Stiles, also known as the Rocky Mountain Wood Tick (RMWT), is found throughout the western United States and transmits pathogens of importance to human and animal health. The distributions and activity patterns of RMWTs are shaped by regional climatic variation. However, it is unknown if responses to climatic variation differ across the tick's geographical range. The objective of this narrow study was to test the hypothesis that the responses of RMWTs to abiotic conditions [e.g. temperature and RH (relative humidity)] vary among populations. We collected RMWTs from ecologically distinct field sites in the states of Montana and Oregon (USA). In the laboratory, we tracked weekly survival of tick larvae under four combinations of RH (75% and 98%) and temperature (26 and 32 °C) that reflected the range of conditions observed in the source habitats during spring-summer. For both populations, larval survival time decreased at the higher ambient temperature (50% mortality 1-2 weeks earlier). Differences in RH did not affect the survival time of larvae from Oregon. By contrast, the survival time of larvae from Montana decreased at the lower RH (50% mortality 1 week earlier). These data suggest that the tolerance limits for water stress may differ among populations of D. andersoni. © 2014 The Royal Entomological Society.

  14. A comparative study of two food model systems to test the survival of Campylobacter jejuni at -18 degrees C

    DEFF Research Database (Denmark)

    Birk, Tina; Rosenquist, Hanne; Brondsted, L.

    2006-01-01

    The survival of Campylobacter jejuni NCTC 11168 was tested at freezing conditions (-18 degrees C) over a period of 32 days in two food models that simulated either (i) the chicken skin surface (skin model) or (ii) the chicken juice in and around a broiler carcass (liquid model). In the skin model...

  15. Minimally invasive esophagectomy provides significant survival advantage compared with open or hybrid esophagectomy for patients with cancers of the esophagus and gastroesophageal junction.

    Science.gov (United States)

    Palazzo, Francesco; Rosato, Ernest L; Chaudhary, Asadulla; Evans, Nathaniel R; Sendecki, Jocelyn A; Keith, Scott; Chojnacki, Karen A; Yeo, Charles J; Berger, Adam C

    2015-04-01

    Minimally invasive esophagectomy (MIE) is increasingly being used to treat patients with cancer of the esophagus and gastroesophageal junction. We previously reported that oncologic efficacy may be improved with MIE compared with open or hybrid esophagectomy (OHE). We compared survival of patients undergoing MIE and OHE. Our contemporary series of patients who underwent MIE (2008 to 2013) was compared with a cohort undergoing OHE (3-hole [n = 39], Ivor Lewis [n = 16], hybrid [n = 13], 2000 to 2013). Summary statistics were calculated by operation type; Kaplan-Meier methods were used to compare survival. Cox regression was used to assess the impact of operation type (MIE vs OHE) on mortality, adjusting for age, sex, total lymph nodes, lymph node ratio (LNR), neoadjuvant chemoradiotherapy (CRT), and stage. The MIE (n = 104) and OHE (n = 68) groups were similar with respect to age and sex. The MIE group tended to have higher BMI, earlier stage disease, and was less likely to receive CRT. The MIE group experienced lower operative mortality (3.9% vs 8.8%, p = 0.35) and significantly fewer major complications. Five-year survival between groups was significantly different (MIE, 64%, OHE, 35%, p analysis demonstrated that patients undergoing OHE had a significantly worse survival compared with MIE independent of age, LNR, CRT, and pathologic stage (hazard ratio 2.00, p = 0.019). This study supports MIE for EC as a superior procedure with respect to overall survival, perioperative mortality, and severity of postoperative complications. Several biases may have affected these results: earlier stage in the MIE group and disparity in timing of the procedures. These results will need to be confirmed in future prospective studies with longer follow-up. Copyright © 2015 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

  16. GLP-1 analogs reduce hepatocyte steatosis and improve survival by enhancing the unfolded protein response and promoting macroautophagy.

    Directory of Open Access Journals (Sweden)

    Shvetank Sharma

    Full Text Available Nonalcoholic fatty liver disease (NAFLD is a known outcome of hepatosteatosis. Free fatty acids (FFA induce the unfolded protein response (UPR or endoplasmic reticulum (ER stress that may induce apoptosis. Recent data indicate ER stress to be a major player in the progression of fatty liver to more aggressive lesions. Autophagy on the other hand has been demonstrated to be protective against ER stress-induced cell death. We hypothesized that exendin-4 (GLP-1 analog treatment of fat loaded hepatocytes can reduce steatosis by autophagy which leads to reduced ER stress-related hepatocyte apoptosis.Primary human hepatocytes were loaded with saturated, cis- and trans-unsaturated fatty acids (palmitic, oleic and elaidic acid respectively. Steatosis, induced with all three fatty acids, was significantly resolved after exendin-4 treatment. Exendin-4 sustained levels of GRP78 expression in fat-loaded cells when compared to untreated fat-loaded cells alone. In contrast, CHOP (C/EBP homologous protein; the penultimate protein that leads to ER stress-related cell death was significantly decreased by exendin-4 in hepatocytes loaded with fatty acids. Finally, exendin-4 in fat loaded hepatocytes clearly promoted gene products associated with macroautophagy as measured by enhanced production of both Beclin-1 and LC3B-II, markers for autophagy; and visualized by transmission electron microscopy (TEM. Similar observations were made in mouse liver lysates after mice were fed with high fat high fructose diet and treated with a long acting GLP-1 receptor agonist, liraglutide.GLP-1 proteins appear to protect hepatocytes from fatty acid-related death by prohibition of a dysfunctional ER stress response; and reduce fatty acid accumulation, by activation of both macro-and chaperone-mediated autophagy. These findings provide a novel role for GLP-1 proteins in halting the progression of more aggressive lesions from underlying steatosis in humans afflicted with NAFLD.

  17. An attempt to understand kidney's protein handling function by comparing plasma and urine proteomes.

    Directory of Open Access Journals (Sweden)

    Lulu Jia

    Full Text Available BACKGROUND: With the help of proteomics technology, the human plasma and urine proteomes, which closely represent the protein compositions of the input and output of the kidney, respectively, have been profiled in much greater detail by different research teams. Many datasets have been accumulated to form "reference profiles" of the plasma and urine proteomes. Comparing these two proteomes may help us understand the protein handling aspect of kidney function in a way, however, which has been unavailable until the recent advances in proteomics technology. METHODOLOGY/PRINCIPAL FINDINGS: After removing secreted proteins downstream of the kidney, 2611 proteins in plasma and 1522 in urine were identified with high confidence and compared based on available proteomic data to generate three subproteomes, the plasma-only subproteome, the plasma-and-urine subproteome, and the urine-only subproteome, and they correspond to three groups of proteins that are handled in three different ways by the kidney. The available experimental molecular weights of the proteins in the three subproteomes were collected and analyzed. Since the functions of the overrepresented proteins in the plasma-and-urine subproteome are probably the major functions that can be routinely regulated by excretion from the kidney in physiological conditions, Gene Ontology term enrichment in the plasma-and-urine subproteome versus the whole plasma proteome was analyzed. Protease activity, calcium and growth factor binding proteins, and coagulation and immune response-related proteins were found to be enriched. CONCLUSION/SIGNIFICANCE: The comparison method described in this paper provides an illustration of a new approach for studying organ functions with a proteomics methodology. Because of its distinctive input (plasma and output (urine, it is reasonable to predict that the kidney will be the first organ whose functions are further elucidated by proteomic methods in the near future. It

  18. Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia.

    Science.gov (United States)

    Gislason, April S; Turner, Keith; Domaratzki, Mike; Cardona, Silvia T

    2017-11-01

    Burkholderia cenocepacia K56-2 belongs to the Burkholderia cepacia complex, a group of Gram-negative opportunistic pathogens that have large and dynamic genomes. In this work, we identified the essential genome of B. cenocepacia K56-2 using high-density transposon mutagenesis and insertion site sequencing (Tn-seq circle). We constructed a library of one million transposon mutants and identified the transposon insertions at an average of one insertion per 27 bp. The probability of gene essentiality was determined by comparing of the insertion density per gene with the variance of neutral datasets generated by Monte Carlo simulations. Five hundred and eight genes were not significantly disrupted, suggesting that these genes are essential for survival in rich, undefined medium. Comparison of the B. cenocepacia K56-2 essential genome with that of the closely related B. cenocepacia J2315 revealed partial overlapping, suggesting that some essential genes are strain-specific. Furthermore, 158 essential genes were conserved in B. cenocepacia and two species belonging to the Burkholderia pseudomallei complex, B. pseudomallei K96243 and Burkholderia thailandensis E264. Porins, including OpcC, a lysophospholipid transporter, LplT, and a protein involved in the modification of lipid A with aminoarabinose were found to be essential in Burkholderia genomes but not in other bacterial essential genomes identified so far. Our results highlight the existence of cell envelope processes that are uniquely essential in species of the genus Burkholderia for which the essential genomes have been identified by Tn-seq.

  19. JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories.

    Science.gov (United States)

    David, Charles C; Singam, Ettayapuram Ramaprasad Azhagiya; Jacobs, Donald J

    2017-05-25

    Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two common approaches to determine PCA modes (eigenvectors) and their eigenvalues. Protein dynamics can be characterized in terms of Cartesian coordinates or internal distance pairs. In understanding protein dynamics, a comparison of trajectories taken from a set of proteins for similarity assessment provides insight into conserved mechanisms. Comprehensive software is needed to facilitate comparative-analysis with user-friendly features that are rooted in best practices from multivariate statistics. We developed a Java based Essential Dynamics toolkit called JED to compare the ED from multiple protein trajectories. Trajectories from different simulations and different proteins can be pooled for comparative studies. JED implements Cartesian-based coordinates (cPCA) and internal distance pair coordinates (dpPCA) as options to construct covariance (Q) or correlation (R) matrices. Statistical methods are implemented for treating outliers, benchmarking sampling adequacy, characterizing the precision of Q and R, and reporting partial correlations. JED output results as text files that include transformed coordinates for aligned structures, several metrics that quantify protein mobility, PCA modes with their eigenvalues, and displacement vector (DV) projections onto the top principal modes. Pymol scripts together with PDB files allow movies of individual Q- and R-cPCA modes to be visualized, and the essential dynamics occurring within user-selected time scales. Subspaces defined by the top eigenvectors are compared using several statistical metrics to quantify similarity/overlap of high dimensional vector spaces. Free energy landscapes can be generated for both cPCA and dpPCA. JED offers a convenient toolkit that encourages best practices in applying multivariate

  20. Reduced selenium-binding protein 1 in breast cancer correlates with poor survival and resistance to the anti-proliferative effects of selenium.

    Directory of Open Access Journals (Sweden)

    Sheng Zhang

    Full Text Available Supplemental dietary selenium is associated with reduced incidence of many cancers. The antitumor function of selenium is thought to be mediated through selenium-binding protein 1 (SELENBP1. However, the significance of SELENBP1 expression in breast cancer is still largely unknown. A total of 95 normal and tumor tissues assay and 12 breast cancer cell lines were used in this study. We found that SELENBP1 expression in breast cancer tissues is reduced compared to normal control. Low SELENBP1 expression in ER(+ breast cancer patients was significantly associated with poor survival (p<0.01, and SELENBP1 levels progressively decreased with advancing clinical stages of breast cancer. 17-β estradiol (E2 treatment of high SELENBP1-expressing ER(+ cell lines led to a down-regulation of SELENBP1, a result that did not occur in ER(- cell lines. However, after ectopic expression of ER in an originally ER(- cell line, down-regulation of SELENBP1 upon E2 treatment was observed. In addition, selenium treatment resulted in reduced cell proliferation in endogenous SELENBP1 high cells; however, after knocking-down SELENBP1, we observed no significant reduction in cell proliferation. Similarly, selenium has no effect on inhibition of cell proliferation in low endogenous SELENBP1 cells, but the inhibitory effect is regained following ectopic SELENBP1 expression. Furthermore, E2 treatment of an ER silenced high endogenous SELENBP1 expressing cell line showed no abolishment of cell proliferation inhibition upon selenium treatment. These data indicate that SELENBP1 expression is regulated via estrogen and that the cell proliferation inhibition effect of selenium treatment is dependent on the high level of SELENBP1 expression. Therefore, the expression level of SELENBP1 could be an important marker for predicting survival and effectiveness of selenium supplementation in breast cancer. This is the first study to reveal the importance of monitoring SELENBP1 expression

  1. Do female cancer patients display better survival rates compared with males? Analysis of the Korean National Registry data, 2005-2009.

    Directory of Open Access Journals (Sweden)

    Kyu-Won Jung

    Full Text Available BACKGROUND: Sex differences have been reported in the prognosis of certain cancers. In this study, we investigated whether Korean females display better survival rates compared with male patients for solid tumor sites. METHODS: We analyzed data from the Korean National Cancer Incidence Database from 599,288 adult patients diagnosed with solid cancers between 2005 and 2009. Patients were followed until December 2010. We applied a relative excess risk (RER model adjusting for year of follow-up, age at diagnosis, and stage at diagnosis. RESULTS: For all solid cancer sites combined, women displayed an 11% lower risk of death compared to men (RER 0.89; 95% CI 0.88-0.90 after adjusting for year of follow-up, age, stage, and case mix. Women showed significantly lower RERs for the following sites: head/neck, esophagus, small intestine, liver, nasal cavities, lung, bone/cartilages, melanoma of skin, soft tissue, brain and CNS, and thyroid. In contrast, women displayed a poorer prognosis than did men for colorectal, laryngeal, kidney and bladder cancer. However, the survival gaps between men and women narrowed by increase in age; female patients over 75 years of age displayed a 3% higher RER of death compared with males in this age group. CONCLUSIONS: Female cancer patients display an improved survival for the majority of solid tumor sites, even after adjustment for age and stage. Age at diagnosis was the major contributor to the women's survival advantage.

  2. Survival and cause of death after transcatheter aortic valve replacement as compared to an age- and sex-matched background population.

    Science.gov (United States)

    Theut, Marie; Thygesen, Julie B; De Backer, Ole; Søndergaard, Lars

    2017-10-13

    This study aimed to assess survival and causes of death in a real-world TAVR population as compared to an age- and sex-matched background population. Each aortic stenosis (AS) patient treated with TAVR in Eastern Denmark between 2007 and 2014 (n=617) was matched with 25 age- and sex-matched controls (n=15,425) randomly drawn from the general Danish population. In the total TAVR population, early mortality (≤90 days) was significantly higher (hazard ratio [HR] 3.90 [2.82-5.39]; ppopulation, driven mainly by cardiovascular (CV) mortality. Late mortality (>90 days) was not different between the TAVR and background population (HR 1.16 [0.96-1.40]; p=0.126), causes of death being mainly non-CV. In subgroup analysis, the HR for late mortality was 0.98, 1.11, and 1.90 for the low-, intermediate-, and high-risk TAVR groups, respectively, as compared to their matched controls and 1.04, 1.45, and 1.52 for the high gradient, paradoxical low-flow low-gradient (P-LFLG), and classical LFLG (C-LFLG) groups, respectively, as compared to their controls. In general, AS patients who survive the first three months after TAVR have a similar survival to their matched controls. Relative survival benefit is the highest in low-to-intermediate risk AS patients with a high transvalvular gradient.

  3. Self-rated health in the last 12 years of life compared to matched surviving controls: the Health and Retirement Study.

    Directory of Open Access Journals (Sweden)

    Sari Stenholm

    Full Text Available Self-rated health (SRH is a valid measure of health status and associated with mortality. Based on individual-level biannual repeat data on SRH we sought to characterize the natural history of poor SRH during the 12 years prior to death in men and women in different age groups. We conducted a retrospective analysis of the Health and Retirement Study participants who died between 1998 and 2010 and had at least two SRH measurements in the 12 years prior to death. We used a nested case-control design to compare SRH trajectories of deceased men and women aged 30-64, 65-79 and 80 years versus surviving participants. The cases comprised 3,350 deceased participants who were matched to surviving controls (n = 8,127. SRH was dichotomized into good vs. poor health. Men and women dying at age 65-79 and ≥ 80 years had 1.5 to 3 times higher prevalence of poor SRH already 11-12 years prior to death compared to surviving controls. The risk estimates remained statistically significant even after adjusting for life-style related risk factors and diagnosed diseases. Prevalence of poor SRH before death was lowest among those aged ≥ 80 years and highest in 30-64 year-olds. In conclusion, men and women who subsequently die perceive their health worse already 11-12 years prior to death compared to their surviving controls.

  4. Long-term survival outcomes by smoking status in surgical and nonsurgical patients with non-small cell lung cancer: comparing never smokers and current smokers.

    Science.gov (United States)

    Meguid, Robert A; Hooker, Craig M; Harris, James; Xu, Li; Westra, William H; Sherwood, J Timothy; Sussman, Marc; Cattaneo, Stephen M; Shin, James; Cox, Solange; Christensen, Joani; Prints, Yelena; Yuan, Nance; Zhang, Jennifer; Yang, Stephen C; Brock, Malcolm V

    2010-09-01

    Survival outcomes of never smokers with non-small cell lung cancer (NSCLC) who undergo surgery are poorly characterized. This investigation compared surgical outcomes of never and current smokers with NSCLC. This investigation was a single-institution retrospective study of never and current smokers with NSCLC from 1975 to 2004. From an analytic cohort of 4,546 patients with NSCLC, we identified 724 never smokers and 3,822 current smokers. Overall, 1,142 patients underwent surgery with curative intent. For survival analysis by smoking status, hazard ratios (HRs) were estimated using Cox proportional hazard modeling and then further adjusted by other covariates. Never smokers were significantly more likely than current smokers to be women (P cancer diagnosis has little impact on the long-term survival of patients with NSCLC, especially after curative surgery. Despite different etiologies between lung cancer in never and current smokers the prognosis is equally dismal.

  5. Niclosamide, an anti-helminthic molecule, downregulates the retroviral oncoprotein Tax and pro-survival Bcl-2 proteins in HTLV-1-transformed T lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, Di [Penn State Hershey Cancer Institute, Penn State University College of Medicine, Hershey, PA 17033 (United States); Yuan, Yunsheng [Penn State Hershey Cancer Institute, Penn State University College of Medicine, Hershey, PA 17033 (United States); Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai (China); Chen, Li [Pharmacy College, Fujian University of Traditional Chinese Medicine, Fuzhou (China); Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201 (United States); Liu, Xin; Belani, Chandra [Penn State Hershey Cancer Institute, Penn State University College of Medicine, Hershey, PA 17033 (United States); Cheng, Hua, E-mail: hcheng@ihv.umaryland.edu [Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201 (United States); Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201 (United States); Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201 (United States); Department Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201 (United States)

    2015-08-14

    Adult T cell leukemia and lymphoma (ATL) is a highly aggressive form of hematological malignancy and is caused by chronic infection of human T cell leukemia virus type 1 (HTLV-1). The viral genome encodes an oncogenic protein, Tax, which plays a key role in transactivating viral gene transcription and in deregulating cellular oncogenic signaling to promote survival, proliferation and transformation of virally infected T cells. Hence, Tax is a desirable therapeutic target, particularly at early stage of HTLV-1-mediated oncogenesis. We here show that niclosamide, an anti-helminthic molecule, induced apoptosis of HTLV-1-transformed T cells. Niclosamide facilitated degradation of the Tax protein in proteasome. Consistent with niclosamide-mediated Tax degradation, this compound inhibited activities of MAPK/ERK1/2 and IκB kinases. In addition, niclosamide downregulated Stat3 and pro-survival Bcl-2 family members such as Mcl-1 and repressed the viral gene transcription of HTLV-1 through induction of Tax degradation. Since Tax, Stat3 and Mcl-1 are crucial molecules for promoting survival and growth of HTLV-1-transformed T cells, our findings demonstrate a novel mechanism of niclosamide in inducing Tax degradation and downregulating various cellular pro-survival molecules, thereby promoting apoptosis of HTLV-1-associated leukemia cells. - Highlights: • Niclosamide is a promising therapeutic candidate for adult T cell leukemia. • Niclosamide employs a novel mechanism through proteasomal degradation of Tax. • Niclosamide downregulates certain cellular pro-survival molecules.

  6. Comparative Analysis of Electrophoretic Profile of Major Proteins of Milk from Alpine and Carpathian Goats

    Directory of Open Access Journals (Sweden)

    Alina NASALEAN

    2017-05-01

    Full Text Available The milk’s proteins provide nutritional and biologically active values, essential in human and animal nutrition. In the case of goat milk, the proteins’ concentration and quality represent basic indices for the evaluation of the nutritional and biologically active values. The proposal is to comparatively analyse the protein profile of milk. The milk was collected from two different breeds: French Alpine and Romanian Carpathian. During March and April 2016 there were collected samples of raw milk in hygienic and sanitation conditions. There were two lots: first lot has 10 Carpathian goats and the second lot has 10 Alpine goats. The protein composition of goat milk was established with SDS-PAGE, after the evaluation of the total proteins’ concentration with the Bradford method. The quantitative and percentage data obtained with electrophoresis revealed few differences between those 8 identified protein fractions. Between those two lots, regarding the levels of β-CN, k-CN and β-lactoglobulines there were significant differences. The other protein fractions have values almost identical. Statistical analysis of obtained data shaped the differences in the protein profile at those two breeds. Based on those differences it is to note the superior potential of the Alpine breed regarding the content in biologically active milk proteins. Regarding the obtained data, this study brings new contributions for the evaluation and analysis of protein profile as a nutritive and biologically active component of goat milk, confirming its character as a functional aliment.

  7. Comparative Proteomic Analysis of Cotton Fiber Development and Protein Extraction Method Comparison in Late Stage Fibers

    Directory of Open Access Journals (Sweden)

    Hana Mujahid

    2016-02-01

    Full Text Available The distinct stages of cotton fiber development and maturation serve as a single-celled model for studying the molecular mechanisms of plant cell elongation, cell wall development and cellulose biosynthesis. However, this model system of plant cell development is compromised for proteomic studies due to a lack of an efficient protein extraction method during the later stages of fiber development, because of a recalcitrant cell wall and the presence of abundant phenolic compounds. Here, we compared the quality and quantities of proteins extracted from 25 dpa (days post anthesis fiber with multiple protein extraction methods and present a comprehensive quantitative proteomic study of fiber development from 10 dpa to 25 dpa. Comparative analysis using a label-free quantification method revealed 287 differentially-expressed proteins in the 10 dpa to 25 dpa fiber developmental period. Proteins involved in cell wall metabolism and regulation, cytoskeleton development and carbohydrate metabolism among other functional categories in four fiber developmental stages were identified. Our studies provide protocols for protein extraction from maturing fiber tissues for mass spectrometry analysis and expand knowledge of the proteomic profile of cotton fiber development.

  8. The AnnoLite and AnnoLyze programs for comparative annotation of protein structures

    Directory of Open Access Journals (Sweden)

    Dopazo Joaquín

    2007-05-01

    Full Text Available Abstract Background Advances in structural biology, including structural genomics, have resulted in a rapid increase in the number of experimentally determined protein structures. However, about half of the structures deposited by the structural genomics consortia have little or no information about their biological function. Therefore, there is a need for tools for automatically and comprehensively annotating the function of protein structures. We aim to provide such tools by applying comparative protein structure annotation that relies on detectable relationships between protein structures to transfer functional annotations. Here we introduce two programs, AnnoLite and AnnoLyze, which use the structural alignments deposited in the DBAli database. Description AnnoLite predicts the SCOP, CATH, EC, InterPro, PfamA, and GO terms with an average sensitivity of ~90% and average precision of ~80%. AnnoLyze predicts ligand binding site and domain interaction patches with an average sensitivity of ~70% and average precision of ~30%, correctly localizing binding sites for small molecules in ~95% of its predictions. Conclusion The AnnoLite and AnnoLyze programs for comparative annotation of protein structures can reliably and automatically annotate new protein structures. The programs are fully accessible via the Internet as part of the DBAli suite of tools at http://salilab.org/DBAli/.

  9. Exploring the function of protein kinases in schistosomes: perspectives from the laboratory and from comparative genomics

    Directory of Open Access Journals (Sweden)

    Anthony John Walker

    2014-07-01

    Full Text Available Eukaryotic protein kinases are well conserved through evolution. The genome of Schistosoma mansoni, which causes intestinal schistosomiasis, encodes over 250 putative protein kinases with all of the main eukaryotic groups represented. However, unraveling functional roles for these kinases is a considerable endeavour, particularly as protein kinases regulate multiple and sometimes overlapping cell and tissue functions in organisms. In this article, elucidating protein kinase signal transduction and function in schistosomes is considered from the perspective of the state-of-the-art methodologies used and comparative organismal biology, with a focus on current advances and future directions. Using the free-living nematode Caenorhabditis elegans as a comparator we predict roles for various schistosome protein kinases in processes vital for host invasion and successful parasitism such as sensory behaviour, growth and development. It is anticipated that the characterization of schistosome protein kinases in the context of parasite function will catalyze cutting edge research into host-parasite interactions and will reveal new targets for developing drug interventions against human schistosomiasis.

  10. Optimizing identification and quantitation of 15N-labeled proteins in comparative proteomics.

    Science.gov (United States)

    Gouw, Joost W; Tops, Bastiaan B J; Mortensen, Peter; Heck, Albert J R; Krijgsveld, Jeroen

    2008-10-15

    Comparative proteomics has emerged as a powerful approach to determine differences in protein abundance between biological samples. The introduction of stable-isotopes as internal standards especially paved the road for quantitative proteomics for comprehensive approaches to accurately determine protein dynamics. Metabolic labeling with (15)N isotopes is applied to an increasing number of organisms, including Drosophila, C. elegans, and rats. However, (15)N-enrichment is often suboptimal (quantitation of proteins. Here, we systematically investigated two independent (15)N-labeled data sets to explore the influence of heavy nitrogen enrichment on the number of identifications as well as on the error in protein quantitation. We show that specifically larger (15)N-labeled peptides are under-represented when compared to their (14)N counterparts and propose a correction method, which significantly increases the number of identifications. In addition, we developed a method that corrects for inaccurate peptide ratios introduced by incomplete (15)N enrichment. This results in improved accuracy and precision of protein quantitation. Altogether, this study provides insight into the process of protein identification and quantitation, and the methods described here can be used to improve both qualitative and quantitative data obtained by labeling with heavy nitrogen with enrichment less than 100%.

  11. Lipoprotein(a) and dietary proteins: casein lowers lipoprotein(a) concentrations as compared with soy protein1-3

    DEFF Research Database (Denmark)

    Nilausen, Karin Johanne; Meinertz, H.

    1999-01-01

    Lipoprotein(a), plasma lipoproteins, dietary proteins, soy protein, casein, liquid-formula, coronary artery disease, men, Denmark......Lipoprotein(a), plasma lipoproteins, dietary proteins, soy protein, casein, liquid-formula, coronary artery disease, men, Denmark...

  12. Nutritional assessment of transgenic lysine-rich maize compared with conventional quality protein maize.

    Science.gov (United States)

    Tang, Maozhi; He, Xiaoyun; Luo, Yunbo; Ma, Liyan; Tang, Xiaoge; Huang, Kunlun

    2013-03-30

    The gene sb401 encoding a lysine-rich protein has been successfully integrated into the genome of maize (Zea mays), its expression showing as increased levels of lysine and total protein in maize seeds. As part of a nutritional assessment of transgenic maize, nutritional composition, especially unintended changes in key nutrients such as proximates, amino acids, minerals and vitamins as well as in antinutrient (phytate phosphorus), and protein nutritional quality were compared between transgenic maize (inbred line 642 and hybrid line Y642) and conventional quality protein maize (QPM) Nongda 108. The contents of total protein, lysine, some other amino acids, several minerals and vitamin B₂ in transgenic inbred line 642 and hybrid line Y642 were significantly higher than those in conventional QPM. Water-soluble protein and G2-glutelin were significantly promoted in transgenic maize Y642. Insertion of the lysine-rich sb401 gene increased the total protein and lysine content of transgenic maize varieties, leading to an improved amino acid score and therefore an improvement in the nutritive value of maize. © 2013 Society of Chemical Industry.

  13. Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae

    DEFF Research Database (Denmark)

    Lavin, J.L.; Kiil, Kristoffer; Resano, O.

    2007-01-01

    requires a complex array of TCS proteins to cope with diverse plant hosts, host responses, and environmental conditions. Results: Based on the genomic data, pattern searches with Hidden Markov Model (HMM) profiles have been used to identify putative HKs and RRs. The genomes of Psy B728a, Pto DC3000 and Pph...... (Pph) 1448A have been recently sequenced providing a major resource for comparative genomic analysis. A mechanism commonly found in bacteria for signal transduction is the two-component system (TCS), which typically consists of a sensor histidine kinase (HK) and a response regulator (RR). P. syringae...... 1448A were found to contain a large number of genes encoding TCS proteins, and a core of complete TCS proteins were shared between these genomes: 30 putative TCS clusters, 11 orphan HKs, 33 orphan RRs, and 16 hybrid HKs. A close analysis of the distribution of genes encoding TCS proteins revealed...

  14. Comparing survival and recurrence in curative stage I to III colorectal cancer in transfused and nontransfused patients.

    Science.gov (United States)

    Talukder, Yumna; Stillwell, Andrew P; Siu, Simon K; Ho, Yik-Hong

    2014-01-01

    Evidence of the association between blood transfusions and its impact on prognostic outcomes in patients who undergo curative resection of colorectal cancer remains controversial. The aim of this study was to determine whether receiving peri-operative blood transfusions during curative colorectal cancer resection affected overall survival, cancer-related survival, and cancer recurrence. This retrospective study was undertaken at The Royal Brisbane and Women's Hospital, Australia, between 1984 and 2004. The outcomes of 1370 patients undergoing curative colorectal cancer resection for TNM stage I to III were analyzed. Four hundred twenty three patients (30.9%) required transfusion and 947 patients (69.1%) did not. Peri-operative transfusion was associated with higher rates of cancer recurrence on multivariate analysis (P = 0.024, RR, 1.257, 95% CI, 1.03-1.53); however, it was not independently associated with poorer overall or cancer-related survival. Where the aim is curative resection, this study contributes to a body of evidence that blood transfusions may be associated with poorer outcomes.

  15. Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions.

    Directory of Open Access Journals (Sweden)

    2005-08-01

    Full Text Available Protein interaction networks are an important part of the post-genomic effort to integrate a part-list view of the cell into system-level understanding. Using a set of 11 yeast genomes we show that combining comparative genomics and secondary structure information greatly increases consensus-based prediction of SH3 targets. Benchmarking of our method against positive and negative standards gave 83% accuracy with 26% coverage. The concept of an optimal divergence time for effective comparative genomics studies was analyzed, demonstrating that genomes of species that diverged very recently from Saccharomyces cerevisiae(S. mikatae, S. bayanus, and S. paradoxus, or a long time ago (Neurospora crassa and Schizosaccharomyces pombe, contain less information for accurate prediction of SH3 targets than species within the optimal divergence time proposed. We also show here that intrinsically disordered SH3 domain targets are more probable sites of interaction than equivalent sites within ordered regions. Our findings highlight several novel S. cerevisiae SH3 protein interactions, the value of selection of optimal divergence times in comparative genomics studies, and the importance of intrinsic disorder for protein interactions. Based on our results we propose novel roles for the S. cerevisiae proteins Abp1p in endocytosis and Hse1p in endosome protein sorting.

  16. Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions.

    Directory of Open Access Journals (Sweden)

    Pedro Beltrao

    2005-08-01

    Full Text Available Protein interaction networks are an important part of the post-genomic effort to integrate a part-list view of the cell into system-level understanding. Using a set of 11 yeast genomes we show that combining comparative genomics and secondary structure information greatly increases consensus-based prediction of SH3 targets. Benchmarking of our method against positive and negative standards gave 83% accuracy with 26% coverage. The concept of an optimal divergence time for effective comparative genomics studies was analyzed, demonstrating that genomes of species that diverged very recently from Saccharomyces cerevisiae(S. mikatae, S. bayanus, and S. paradoxus, or a long time ago (Neurospora crassa and Schizosaccharomyces pombe, contain less information for accurate prediction of SH3 targets than species within the optimal divergence time proposed. We also show here that intrinsically disordered SH3 domain targets are more probable sites of interaction than equivalent sites within ordered regions. Our findings highlight several novel S. cerevisiae SH3 protein interactions, the value of selection of optimal divergence times in comparative genomics studies, and the importance of intrinsic disorder for protein interactions. Based on our results we propose novel roles for the S. cerevisiae proteins Abp1p in endocytosis and Hse1p in endosome protein sorting.

  17. Comparative Survival Study (CSS) of Hatchery PIT-tagged Spring/Summer Chinook; Migration Years 1997-2000 Mark/Recapture Activities, 2001 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Bouwes, Nick (EcoLogical Research, Providence, UT); Petrosky, Charlie (Idaho Department of Fish and Game, Boise ID); Schaller, Howard (US Fish and Wildlife Service, Columbia River Fisheries Program Office, Vancouver, WA)

    2002-02-01

    The Comparative Survival Study (CSS) was initiated in 1996 as a multi-year program of the fishery agencies and tribes to estimate survival rates over different life stages for spring and summer chinook (hereafter, chinook) produced in major hatcheries in the Snake River basin and from selected hatcheries in the lower Columbia River. Much of the information evaluated in the CSS is derived from fish tagged with Passive Integrated Transponder (PIT) tags. A comparison of survival rates of chinook marked in two different regions (which differ in the number of dams chinook have to migrate through) provides insight into the effects of the Snake/Columbia hydroelectric system (hydrosystem). The CSS also compares the smolt-to-adult survival rates (SARs) for Snake River chinook that were transported versus those that migrated in-river to below Bonneville Dam. Additional comparisons can be made within in-river experiences as well comparison between the different collector projects from which smolts are transported. CSS also compares these survival rates for wild Snake River spring and summer chinook. These comparisons generate information regarding the relative effects of the current management actions used to recover this listed species.Scientists and managers have recently emphasized the importance of delayed hydrosystem mortality to long-term management decisions. Delayed hydrosystem mortality may be related to the smolts. experience in the Federal Columbia River Power System, and could occur for both smolts that migrate in-river and smolts that are transported. The CSS PIT tag information on in-river survival rates and smolt-to-adult survival rates (SARs) of transported and in-river fish are relevant to estimation of ''D'', which partially describes delayed hydrosystem mortality. ''D'', or differential delayed mortality, is the differential survival rate of transported fish relative to fish that migrate in-river, as measured from

  18. Proteomic Profiling Comparing the Effects of Different Heat Treatments on Camel (Camelus dromedarius) Milk Whey Proteins.

    Science.gov (United States)

    Benabdelkamel, Hicham; Masood, Afshan; Alanazi, Ibrahim O; Alzahrani, Dunia A; Alrabiah, Deema K; AlYahya, Sami A; Alfadda, Assim A

    2017-03-28

    Camel milk is consumed in the Middle East because of its high nutritional value. Traditional heating methods and the duration of heating affect the protein content and nutritional quality of the milk. We examined the denaturation of whey proteins in camel milk by assessing the effects of temperature on the whey protein profile at room temperature (RT), moderate heating at 63 °C, and at 98 °C, for 1 h. The qualitative and quantitative variations in the whey proteins before and after heat treatments were determined using quantitative 2D-difference in gel electrophoresis (DIGE)-mass spectrometry. Qualitative gel image analysis revealed a similar spot distribution between samples at RT and those heated at 63 °C, while the spot distribution between RT and samples heated at 98 °C differed. One hundred sixteen protein spots were determined to be significantly different (p milk samples. Eighty protein spots were decreased in common in both the heat-treated samples and an additional 25 spots were further decreased in the 98 °C sample. The proteins with decreased abundance included serum albumin, lactadherin, fibrinogen β and γ chain, lactotransferrin, active receptor type-2A, arginase-1, glutathione peroxidase-1 and, thiopurine S, etc. Eight protein spots were increased in common to both the samples when compared to RT and included α-lactalbumin, a glycosylation-dependent cell adhesion molecule. Whey proteins present in camel milk were less affected by heating at 63 °C than at 98 °C. This experimental study showed that denaturation increased significantly as the temperature increased from 63 to 98 °C.

  19. Proteomic Profiling Comparing the Effects of Different Heat Treatments on Camel (Camelus dromedarius) Milk Whey Proteins

    Science.gov (United States)

    Benabdelkamel, Hicham; Masood, Afshan; Alanazi, Ibrahim O.; Alzahrani, Dunia A.; Alrabiah, Deema K.; AlYahya, Sami A.; Alfadda, Assim A.

    2017-01-01

    Camel milk is consumed in the Middle East because of its high nutritional value. Traditional heating methods and the duration of heating affect the protein content and nutritional quality of the milk. We examined the denaturation of whey proteins in camel milk by assessing the effects of temperature on the whey protein profile at room temperature (RT), moderate heating at 63 °C, and at 98 °C, for 1 h. The qualitative and quantitative variations in the whey proteins before and after heat treatments were determined using quantitative 2D-difference in gel electrophoresis (DIGE)-mass spectrometry. Qualitative gel image analysis revealed a similar spot distribution between samples at RT and those heated at 63 °C, while the spot distribution between RT and samples heated at 98 °C differed. One hundred sixteen protein spots were determined to be significantly different (p milk samples. Eighty protein spots were decreased in common in both the heat-treated samples and an additional 25 spots were further decreased in the 98 °C sample. The proteins with decreased abundance included serum albumin, lactadherin, fibrinogen β and γ chain, lactotransferrin, active receptor type-2A, arginase-1, glutathione peroxidase-1 and, thiopurine S, etc. Eight protein spots were increased in common to both the samples when compared to RT and included α-lactalbumin, a glycosylation-dependent cell adhesion molecule. Whey proteins present in camel milk were less affected by heating at 63 °C than at 98 °C. This experimental study showed that denaturation increased significantly as the temperature increased from 63 to 98 °C. PMID:28350354

  20. Comparative study of RBE and cell survival fractions for $^{1}$H, $^{4}$He, $^{12}$C and $^{16}$O beams using Geant4 and Microdosimetric Kinetic model

    CERN Document Server

    Burigo, Lucas; Mishustin, Igor; Bleicher, Marcus

    2014-01-01

    Beams of $^{4}$He and $^{16}$O nuclei are considered for ion-beam cancer therapy as alternative options to protons and $^{12}$C nuclei. Spread-out Bragg peak (SOBP) distributions of physical dose and relative biological effectiveness for 10% survival are calculated by means of our Geant4-based Monte Carlo model for Heavy Ion Therapy (MCHIT) and the modified microdosimetric kinetic model. The depth distributions of cell survival fractions are calculated for $^{1}$H, $^{4}$He, $^{12}$C and $^{16}$O for tissues with normal (HSG cells), low and high radiosensitivity. In each case the cell survival fractions were compared separately for the target volume, behind and in front of it. In the case of normal radiosensitivity $^{4}$He and $^{12}$C better spare tissues in the entrance channel compared to protons and $^{16}$O. The cell survival fractions calculated, respectively, for the entrance channel and target volume are similar for $^{4}$He and $^{12}$C. When it is important to spare healthy tissues located after th...

  1. Genetic variation in C-reactive protein in relation to colon and rectal cancer risk and survival.

    Science.gov (United States)

    Slattery, Martha L; Curtin, Karen; Poole, Elizabeth M; Duggan, David J; Samowitz, Wade S; Peters, Ulrike; Caan, Bette J; Potter, John D; Ulrich, Cornelia M

    2011-06-01

    C-reactive protein (CRP), a biomarker of inflammation, has been shown to be influenced by genetic variation in the CRP gene. In this study, we test the hypothesis that genetic variation in CRP influences both the risk of developing colon and rectal cancer and survival. Two population-based studies of colon cancer (n = 1,574 cases, 1,970 controls) and rectal (n = 791 cases, 999 controls) were conducted. We evaluated four CRP tagSNPs: rs1205 (G > A, 3' UTR); rs1417938 (T > A, intron); rs1800947 (G > C, L184L); and rs3093075 (C > A, 3' flanking). The CRP rs1205 AA genotype was associated with an increased risk of colon cancer (OR 1.3, 95%CI 1.1-1.7), whereas the rs3093075 A allele was associated with a reduced risk of rectal cancer (OR 0.7, 95%CI 0.5-0.9). The strongest association for the rs1205 polymorphism and colon cancer was observed among those with KRAS2 mutations (OR 1.5, 95%CI 1.1-2.0). The CRP rs1205 AA genotype also was associated with an increased risk of CIMP+ rectal tumors (OR 2.5, 95%CI 1.2-5.3); conversely, the rs1417938 A allele was associated with a reduced risk of CIMP+ rectal tumors (OR 0.5, 95%CI 0.3-0.9). We observed interactions between CRP rs1800947 and BMI and family history of CRC in modifying risk of both colon and rectal cancer. These data suggest that genetic variation in the CRP gene influences risk of both colon and rectal cancer development. Copyright © 2010 UICC.

  2. The polysialic acid mimetics idarubicin and irinotecan stimulate neuronal survival and neurite outgrowth and signal via protein kinase C.

    Science.gov (United States)

    Loers, Gabriele; Astafiev, Steven; Hapiak, Yuliya; Saini, Vedangana; Mishra, Bibhudatta; Gul, Sheraz; Kaur, Gurcharan; Schachner, Melitta; Theis, Thomas

    2017-08-01

    Polysialic acid (PSA) is a large, negatively charged, linear homopolymer of alpha2-8-linked sialic acid residues. It is generated by two polysialyltransferases and attached to N- and/or O-linked glycans, and its main carrier is the neural cell adhesion molecule (NCAM). PSA controls the development and regeneration of the nervous system by enhancing cell migration, axon pathfinding, synaptic targeting, synaptic plasticity, by regulating the differentiation of progenitor cells and by modulating cell-cell and cell-matrix adhesions. In the adult, PSA plays a role in the immune system, and PSA mimetics promote functional recovery after nervous system injury. In search for novel small molecule mimetics of PSA that are applicable for therapy, we identified idarubicin, an antineoplastic anthracycline, and irinotecan, an antineoplastic agent of the topoisomerase I inhibitor class, as PSA mimetics using a competition enzyme-linked immunosorbent assay. Idarubicin and irinotecan compete with the PSA-mimicking peptide and colominic acid, the bacterial analog of PSA, for binding to the PSA-specific monoclonal antibody 735. Idarubicin and irinotecan stimulate neurite outgrowth and survival of cultured cerebellar neurons after oxidative stress via protein kinase C and Erk1/2 in a similar manner as colominic acid, whereas Fyn, casein kinase II and the phosphatase and tensin homolog are only involved in idarubicin and irinotecan-stimulated neurite outgrowth. These novel results show that the structure and function of PSA can be mimicked by the small organic compounds irinotecan and idarubicin which trigger the same signaling cascades as PSA, thus introducing the possibility of retargeting these drugs to treat nervous system injuries. © 2017 International Society for Neurochemistry.

  3. Cancer Cell-derived Exosomes Induce Mitogen-activated Protein Kinase-dependent Monocyte Survival by Transport of Functional Receptor Tyrosine Kinases*

    Science.gov (United States)

    Song, Xiao; Ding, Yanping; Liu, Gang; Yang, Xiao; Zhao, Ruifang; Zhang, Yinlong; Zhao, Xiao; Anderson, Gregory J.; Nie, Guangjun

    2016-01-01

    Tumor-associated macrophages (TAM) play pivotal roles in cancer initiation and progression. Monocytes, the precursors of TAMs, normally undergo spontaneous apoptosis within 2 days, but can subsist in the inflammatory tumor microenvironment for continuous survival and generation of sufficient TAMs. The mechanisms underlying tumor-driving monocyte survival remain obscure. Here we report that cancer cell-derived exosomes were crucial mediators for monocyte survival in the inflammatory niche. Analysis of the survival-promoting molecules in monocytes revealed that cancer cell-derived exosomes activated Ras and extracellular signal-regulated kinases in the mitogen-activated protein kinase (MAPK) pathway, resulting in the prevention of caspase cleavage. Phosphorylated receptor tyrosine kinases (RTKs), such as phosphorylated epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER-2), were abundantly expressed in cancer cell-derived exosomes. Knock-out of EGFR or/and HER-2, or alternatively, inhibitors against their phosphorylation significantly disturbed the exosome-mediated activation of the MAPK pathway, inhibition of caspase cleavage, and increase in survival rate in monocytes. Moreover, the deprived survival-stimulating activity of exosomes due to null expression of EGFR and HER-2 could be restored by activation of another RTK, insulin receptor. Overall, our study uncovered a mechanism of tumor-associated monocyte survival and demonstrated that cancer cell-derived exosomes can stimulate the MAPK pathway in monocytes through transport of functional RTKs, leading to inactivation of apoptosis-related caspases. This work provides insights into the long sought question on monocyte survival prior to formation of plentiful TAMs in the tumor microenvironment. PMID:26895960

  4. Survival of the fittest clone: Pro-apoptotic protein Noxa controls selection of lymphocytes under competitive conditions

    NARCIS (Netherlands)

    Wensveen, F.M.

    2010-01-01

    Darwinistic selection, or ‘survival of the fittest’, is based on intrinsic capacity, relative to that of its competitors in a given niche. This process drives the generation of species by allowing survival of organisms in with favorable, specialized characteristics for a certain niche. However, mere

  5. Increased ID4 expression, accompanied by mutant p53 accumulation and loss of BRCA1/2 proteins in triple-negative breast cancer, adversely affects survival.

    Science.gov (United States)

    Thike, Aye A; Tan, Puay H; Ikeda, Murasaki; Iqbal, Jabed

    2016-04-01

    Breast cancer 1 (BRCA1) expression is down-regulated in a significant proportion of non-hereditary breast cancers, in the absence of any mutation. This phenomenon is more pronounced in oestrogen (ER)-negative tumours. Recent studies have suggested that inhibitor of DNA binding 4 (ID4), as well as p53, participate in the transcriptional regulation of BRCA1. Immunohistochemical expression of ID4, BRCA1, BRCA2 and p53 in 699 women with triple-negative breast cancer was investigated using tissue microarrays. The prognostic role of these biomarkers was also evaluated. Survival outcomes were estimated with the Kaplan-Meier method and compared between groups with log-rank statistics. Loss of BRCA1 and BRCA2 expression and overexpression of ID4 and p53 was observed in 75%, 90%, 95% and 66% of tumours, respectively. ID4 expression was increased in higher tumour grade (P P P = 0.037) and p53 accumulation (P triple-negative breast cancers (P = 0.041) and basal-like triple-negative breast cancers (P = 0.026). There is frequent ID4 expression and concomitant loss of BRCA proteins in triple-negative breast cancer. We hypothesize that strong ID4 expression could be useful as a prognostic marker in triple-negative breast cancer, predicting early tumour recurrence. © 2015 John Wiley & Sons Ltd.

  6. Combined effect of brain-derived neurotrophic factor and LINGO-1 fusion protein on long-term survival of retinal ganglion cells in chronic glaucoma.

    Science.gov (United States)

    Fu, Q-L; Li, X; Yip, H K; Shao, Z; Wu, W; Mi, S; So, K-F

    2009-08-18

    Glaucoma is a progressive neuropathy characterized by loss of vision as a result of retinal ganglion cell (RGC) death. There are no effective neuroprotectants to treat this disorder. Brain-derived neurotrophic factor (BDNF) is well known to transiently delay RGC death in ocular hypertensive eyes. The CNS-specific leucine-rich repeat protein LINGO-1 contributes to the negative regulation to some trophic pathways. We thereby examined whether BDNF combined with LINGO-1 antagonists can promote long-term RGC survival after ocular hypertension. In this study, intraocular pressure was elevated in adult rats using an argon laser to photocoagulate the episcleral and limbal veins. BDNF alone shows slight neuroprotection to RGCs after a long-term progress of 4 weeks following the induction of ocular hypertension. However, combination of BDNF and LINGO-1-Fc prevents RGC death in the same condition. We further identified that (1) LINGO-1 was co-expressed with BDNF receptor, TrkB in the RGCs, and (2) BDNF combined with LINGO-1-Fc activated more TrkB in the injured retina compared to BDNF alone. These results indicate that the combination of BDNF with LINGO-1 antagonist can provide long-term protection for RGCs in a chronic ocular hypertension model. TrkB may be the predominant mediator of this neuroprotection.

  7. Pancreatic cancer and predictors of survival: comparing the CA 19-9/bilirubin ratio with the McGill Brisbane Symptom Score.

    Science.gov (United States)

    Dumitra, Sinziana; Jamal, Mohammad H; Aboukhalil, Jad; Doi, Suhail A; Chaudhury, Prosanto; Hassanain, Mazen; Metrakos, Peter P; Barkun, Jeffrey S

    2013-12-01

    Few tools predict survival from pancreatic cancer (PAC). The McGill Brisbane Symptom Score (MBSS) based on symptoms at presentation (weight loss, pain, jaundice and smoking) was recently validated. The present study compares the ability of four strategies to predict 9-month survival: MBSS, carbohydrate antigen 19-9 (CA 19-9) alone, CA19-9-to-bilirubin ratio and a combination of MBSS and the CA19-9-to-bilirubin ratio. A retrospective review of 133 patients diagnosed with PAC between 2005 and 2011 was performed. Survival was determined from the Quebec civil registry. Blood CA 19-9 and bilirubin values were collected (n = 52) at the time of diagnosis. Receiver-operating characteristic (ROC) curves were used to determine a cutoff for optimal test characteristics of CA 19-9 and CA19-9-to-total bilirubin ratio in predicting survival at 9 months. Predictive characteristics were then calculated for the four strategies. Of the four strategies, the one with the greatest negative predictive value was the MBSS: negative predictive value (NPV) was 90.2% (76.9-97.3%) and the positive likelihood ratio (LR) was the greatest. The ability of CA 19-9 levels alone, at baseline, to predict survival was low. For the CA19-9-to-bilirubin ratio, the test characteristics improved but remained non-significant. The best performing strategy according to likelihood ratios was the combined MBSS and CA19-9 to the bilirubin ratio. CA19-9 levels and the CA19-9-to-bilirubin ratio are poor predictors of survival for PAC, whereas the MBSS is a far better predictor, confirming its clinical value. By adding the CA19-9-to-bilirubin ratio to the MBSS the predictive characteristics improved. © 2013 International Hepato-Pancreato-Biliary Association.

  8. Role of presepsin compared to C-reactive protein in sepsis diagnosis and prognostication

    Directory of Open Access Journals (Sweden)

    Mohamed El-Saied El-Shafie

    2017-04-01

    Full Text Available Early identification of sepsis and its differentiation from non-infective SIRS are important for sepsis outcome. We intended to evaluate the use of presepsin in differentiating sepsis from noninfectious SIRS and its prognostic value compared to CRP. We included 31 patients (median age 60 year old, 16 males admitted with SIRS to El-Sahel Teaching Hospital, Egypt after excluding 21 patients with preadmission corticosteroids therapy, blood transfusion, immunosuppressive illness, and ICU length of stay (ICU-LOS less than 24-hours. Patients were classified into non-infective SIRS group (13 patients and sepsis group (18 patients. Presepsin, CRP and SOFA score were measured on admission and on days 2 and 4 of admission. The outcome parameters studied were ICU-LOS and in-hospital survival. Apart from temperature and AST which were significantly higher in sepsis group, the two groups were comparable. All the presepsin levels and CRP on days 2 and 4 were significantly higher in sepsis than in SIRS groups. The ICU-LOS was positively correlated with all the presepsin levels and with the CRP levels on days 2 and 4. All presepsin values were significantly higher in survivors while none of the CRP levels were significantly different in survivors and non-survivors. The decrease of presepsin over time was significantly associated with better survival. It was found to be 70% sensitive and 91% specific for predicting survival in SIRS patients. This relation was not found in CRP levels. We concluded that the presepsin can be used for early differentiation between sepsis and non-infectious SIRS and predict higher mortality.

  9. Structural dynamics and inhibitor searching for Wnt-4 protein using comparative computational studies

    Directory of Open Access Journals (Sweden)

    Hammad MA

    2015-04-01

    Full Text Available Mirza A Hammad, Syed Sikander Azam National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan Abstract: Wnt-4 (wingless mouse mammary tumor virus integration site-4 protein is involved in many crucial embryonic pathways regulating essential processes. Aberrant Wnt-4 activity causes various anomalies leading to gastric, colon, or breast cancer. Wnt-4 is a conserved protein in structure and sequence. All Wnt proteins contain an unusual fold comprising of a thumb (or N-terminal domain and index finger (or C-terminal domain bifurcated by a palm domain. The aim of this study was to identify the best inhibitors of Wnt-4 that not only interact with Wnt-4 protein but also with the covalently bound acyl group to inhibit aberrant Wnt-4 activity. A systematic computational approach was used to analyze inhibition of Wnt-4. Palmitoleic acid was docked into Wnt-4 protein, followed by ligand-based virtual screening of nearly 209,847 compounds; conformer generation of 271 compounds resulted from extensive virtual screening and comparative docking of 10,531 conformers of 271 unique compounds through GOLD (Genetic Optimization for Ligand Docking, AutoDock-Vina, and FRED (Fast Rigid Exhaustive Docking was subsequently performed. Linux scripts was used to handle the libraries of compounds. The best compounds were selected on the basis of having maximum interactions to protein with bound palmitoleic acid. These represented lead inhibitors in further experiments. Palmitoleic acid is important for efficient Wnt activity, but aberrant Wnt-4 expression can be inhibited by designing inhibitors interacting with both protein and palmitoleic acid. Keywords: thumb-index fold, comparative study, natural products, inhibitor searching, cancer, molecular docking, virtual screening

  10. Comparative immunoblot analysis with 10 different, partially overlapping recombinant fusion proteins derived from 5 different cytomegalovirus proteins

    NARCIS (Netherlands)

    van Zanten, J.; LAZZAROTTO, T; CAMPISI, B; VORNHAGEN, R; JAHN, G; LANDINI, MP; The, T. Hauw

    Ten fusion proteins derived from five various CMV encoded proteins were used for the detection of specific antibody response by immunoblot technique in sera from renal transplant recipients. The fusion proteins were derived from the following CMV specific proteins: the assembly protein ppUL80a with

  11. Lower Superoxide Dismutase 2 (SOD2 Protein Content in Mononuclear Cells Is Associated with Better Survival in Patients with Hemodialysis Therapy

    Directory of Open Access Journals (Sweden)

    Katharina Krueger

    2016-01-01

    Full Text Available Mitochondrial superoxide dismutase 2 (SOD2 converts superoxide anions to hydrogen peroxide and oxygen. Human data on SOD2 protein content in chronic kidney disease (CKD are sparse and mortality data are lacking. We investigated SOD2 protein content in monocytes from patients with hemodialysis therapy (n=81, CKD stage 1–5 (n=120, and healthy controls (n=13 using in-cell Western assays. SOD2 protein decreased from CKD stage 1 until stage 4 whereas it increased again in stage 5 with and without hemodialysis. SOD2 gene expression, analyzed by quantitative real-time PCR, was not significantly different between the groups. Elevating cellular superoxide production reduced SOD2 protein content. This effect was abolished by the superoxide dismutase mimetic Tempol. Using gelelectrophoresis and Western blot we did not detect nitrotyrosine modifications of SOD2 in CKD. Finally, in patients with CKD stage 5 with hemodialysis therapy higher than median SOD2 protein content was associated with higher all-cause mortality. In conclusion, SOD2 protein content declined in CKD until stage 4 while SOD2 gene expression did not. Increased cellular superoxide anion production might affect SOD2 protein content. In advanced CKD (stage 5 SOD2 protein content increased again, but higher than median SOD2 protein content in these patients did not confer a survival benefit.

  12. A comparative study of machine learning methods for time-to-event survival data for radiomics risk modelling.

    Science.gov (United States)

    Leger, Stefan; Zwanenburg, Alex; Pilz, Karoline; Lohaus, Fabian; Linge, Annett; Zöphel, Klaus; Kotzerke, Jörg; Schreiber, Andreas; Tinhofer, Inge; Budach, Volker; Sak, Ali; Stuschke, Martin; Balermpas, Panagiotis; Rödel, Claus; Ganswindt, Ute; Belka, Claus; Pigorsch, Steffi; Combs, Stephanie E; Mönnich, David; Zips, Daniel; Krause, Mechthild; Baumann, Michael; Troost, Esther G C; Löck, Steffen; Richter, Christian

    2017-10-16

    Radiomics applies machine learning algorithms to quantitative imaging data to characterise the tumour phenotype and predict clinical outcome. For the development of radiomics risk models, a variety of different algorithms is available and it is not clear which one gives optimal results. Therefore, we assessed the performance of 11 machine learning algorithms combined with 12 feature selection methods by the concordance index (C-Index), to predict loco-regional tumour control (LRC) and overall survival for patients with head and neck squamous cell carcinoma. The considered algorithms are able to deal with continuous time-to-event survival data. Feature selection and model building were performed on a multicentre cohort (213 patients) and validated using an independent cohort (80 patients). We found several combinations of machine learning algorithms and feature selection methods which achieve similar results, e.g. C-Index = 0.71 and BT-COX: C-Index = 0.70 in combination with Spearman feature selection. Using the best performing models, patients were stratified into groups of low and high risk of recurrence. Significant differences in LRC were obtained between both groups on the validation cohort. Based on the presented analysis, we identified a subset of algorithms which should be considered in future radiomics studies to develop stable and clinically relevant predictive models for time-to-event endpoints.

  13. Whey protein delays gastric emptying and suppresses plasma fatty acids and their metabolites compared to casein, gluten, and fish protein

    DEFF Research Database (Denmark)

    Stanstrup, Jan; Schou, Simon S; Holmer-Jensen, Jens

    2014-01-01

    Whey protein has been demonstrated to improve fasting lipid and insulin response in overweight and obese individuals. To establish new hypotheses for this effect and to investigate the impact of stomach emptying, we compared plasma profiles after intake of whey isolate (WI), casein, gluten (GLU...... studies, the WI meal caused a decreased rate of gastric emptying compared to the other test meals. The WI meal also caused elevated levels of a number of amino acids, possibly stimulating insulin release leading to reduced plasma glucose. The WI meal also caused decreased levels of a number of fatty acids......, while the GLU meal caused elevated levels of a number of unidentified hydroxy fatty acids and dicarboxylic fatty acids. Also reported are a number of markers of fish intake unique to the COD meal....

  14. Combined sequential use of HAP and ART scores to predict survival outcome and treatment failure following chemoembolization in hepatocellular carcinoma: a multi-center comparative study.

    Science.gov (United States)

    Pinato, David J; Arizumi, Tadaaki; Jang, Jeong Won; Allara, Elias; Suppiah, Puvan I; Smirne, Carlo; Tait, Paul; Pai, Madhava; Grossi, Glenda; Kim, Young Woon; Pirisi, Mario; Kudo, Masatoshi; Sharma, Rohini

    2016-07-12

    The prognosis of patients with hepatocellular carcinoma (HCC) undergoing transarterial chemoembolization (TACE) is variable, despite a myriad of prognostic markers. We compared and integrated the established prognostic models, HAP and ART scores, for their accuracy of overall survival (OS) prediction. In both training and validation sets, HAP and ART scores emerged as independent predictors of OS (pfailure. BCLC-C patients with low HAP stage may be a subgroup where TACE should be explored in clinical studies.

  15. Long-term survival results of a randomized trial comparing gemcitabine plus cisplatin, with methotrexate, vinblastine, doxorubicin, plus cisplatin in patients with bladder cancer

    DEFF Research Database (Denmark)

    Maase, Hans von der; Sengeløv, Lisa; Roberts, James T.

    2005-01-01

    PURPOSE: To compare long-term survival in patients with locally advanced       or metastatic transitional cell carcinoma (TCC) of the urothelium treated       with gemcitabine/cisplatin (GC) or       methotrexate/vinblastine/doxorubicin/cisplatin (MVAC). PATIENTS AND       METHODS: Efficacy data...... in patients with locally advanced or       metastatic TCC...

  16. Long-term survival results of a randomized trial comparing gemcitabine/cisplatin and methotrexate/vinblastine/doxorubicin/cisplatin in patients with locally advanced and metastatic bladder cancer

    DEFF Research Database (Denmark)

    Roberts, J T; von der Maase, H; Sengeløv, L

    2006-01-01

    PURPOSE: To compare long-term survival in patients with locally advanced and metastatic transitional cell carcinoma (TCC) of the urothelium treated with gemcitabine plus cisplatin (GC) or methotrexate/vinblastine/doxorubicin/cisplatin (MVAC). PATIENTS AND METHODS: Efficacy data from a large....... These results strengthen the role of GC as a standard of care in patients with locally advanced and metastatic transitional-cell carcinoma (TCC)....

  17. Niclosamide, an anti-helminthic molecule, downregulates the retroviral oncoprotein Tax and pro-survival Bcl-2 proteins in HTLV-1-transformed T lymphocytes.

    Science.gov (United States)

    Xiang, Di; Yuan, Yunsheng; Chen, Li; Liu, Xin; Belani, Chandra; Cheng, Hua

    2015-08-14

    Adult T cell leukemia and lymphoma (ATL) is a highly aggressive form of hematological malignancy and is caused by chronic infection of human T cell leukemia virus type 1 (HTLV-1). The viral genome encodes an oncogenic protein, Tax, which plays a key role in transactivating viral gene transcription and in deregulating cellular oncogenic signaling to promote survival, proliferation and transformation of virally infected T cells. Hence, Tax is a desirable therapeutic target, particularly at early stage of HTLV-1-mediated oncogenesis. We here show that niclosamide, an anti-helminthic molecule, induced apoptosis of HTLV-1-transformed T cells. Niclosamide facilitated degradation of the Tax protein in proteasome. Consistent with niclosamide-mediated Tax degradation, this compound inhibited activities of MAPK/ERK1/2 and IκB kinases. In addition, niclosamide downregulated Stat3 and pro-survival Bcl-2 family members such as Mcl-1 and repressed the viral gene transcription of HTLV-1 through induction of Tax degradation. Since Tax, Stat3 and Mcl-1 are crucial molecules for promoting survival and growth of HTLV-1-transformed T cells, our findings demonstrate a novel mechanism of niclosamide in inducing Tax degradation and downregulating various cellular pro-survival molecules, thereby promoting apoptosis of HTLV-1-associated leukemia cells. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Continuous Veno-Venous Hemofiltration Improves Survival of Patients With Congestive Heart Failure and Cardiorenal Syndrome Compared to Slow Continuous Ultrafiltration.

    Science.gov (United States)

    Premuzic, Vedran; Basic-Jukic, Nikolina; Jelakovic, Bojan; Kes, Petar

    2017-06-01

    Continuous veno-venous hemofiltration (CVVH) could modulate the inflammatory response by removal of circulating cytokines and therefore improve cardiac function in patients with heart failure (HF). We hypothesized that patients with developed cardiorenal syndrome and treated with CVVH have lower risk for mortality than other patients treated with slow continuous ultrafiltration (SCUF). This was a prospective, longitudinal follow-up study for 24 months duration. In total, 120 patients were recruited from the intensive care units. Only patients with cardiorenal syndrome type 1 and 2 were enrolled. 54 CVVH and 23 SCUF patients survived. Mean survival time was longer in CVVH group with cardiomyopathy than in the SCUF group. When we compared patients with cardiomyopathy and hourly urine output cardiorenal syndrome. Better survival in patients treated with CVVH, which is mostly pronounced in patients with cardiomyopathy, is a consequence of a better preserved hourly urine output. Longer survival in patients with cardiomyopathy is most probably related to cytokine removal by CVVH with smaller UF rates and longer duration of each treatment. Slow continuous ultrafiltration remains the method of choice in patients with HF and preserved renal function but in cases of developed cardiorenal syndrome is much inferior to CVVH. © 2017 International Society for Apheresis, Japanese Society for Apheresis, and Japanese Society for Dialysis Therapy.

  19. Retrospective comparative ten-year study of cumulative survival rates of remaining teeth in large edentulism treated with implant-supported fixed partial dentures or removable partial dentures.

    Science.gov (United States)

    Yamazaki, Seiya; Arakawa, Hikaru; Maekawa, Kenji; Hara, Emilio Satoshi; Noda, Kinji; Minakuchi, Hajime; Sonoyama, Wataru; Matsuka, Yoshizo; Kuboki, Takuo

    2013-07-01

    This study aimed to compare the survival rates of remaining teeth between implant-supported fixed dentures (IFDs) and removable partial dentures (RPDs) in patients with large edentulous cases. The second goal was to assess the risk factors for remaining tooth loss. The study subjects were selected among those who received prosthodontic treatment at Okayama University Dental Hospital for their edentulous space exceeding at least four continuous missing teeth. Twenty-one patients were included in the IFD group and 82 patients were included in the RPD group. Survival rates of remaining teeth were calculated in three subcategories: (1) whole remaining teeth, (2) adjacent teeth to intended edentulous space, and (3) opposing teeth to intended edentulous space. The ten-year cumulative survival rate of the whole remaining teeth was significantly higher in the IFD group (40.0%) than in the RPD group (24.4%). On the other hand, there was no significant difference between two groups in the survival rate of teeth adjacent or opposing to intended edentulous space. A Cox proportional hazard analysis revealed that RPD restoration and gender (male) were the significant risk factors for remaining tooth loss (whole remaining teeth). These results suggest that IFD treatment can reduce the incidence of remaining tooth loss in large edentulous cases. Copyright © 2013 Japan Prosthodontic Society. Published by Elsevier Ltd. All rights reserved.

  20. [Determination of proteins with the Coomassie brilliant blue G 250 method. III. Behavior of various pure proteins and comparative analysis with the biuret and Lowry methods].

    Science.gov (United States)

    Serra, S; Morgante, L

    1980-03-15

    Some proteins were tested by the Bradford's method with Coomassie Brilliant Blue G 250. The findings were compared to those obtained by the Lowry's and the biuret methods. Coomassie, as the other methods, has the inconvenient of giving different absorbaces according to the nature of single protein. The use of standards of analogous composition in assaying proteins by the Bradford's method is suggested.

  1. Low HIP1R mRNA and protein expression are associated with worse survival in diffuse large B-cell lymphoma patients treated with R-CHOP

    DEFF Research Database (Denmark)

    Wong, K. K.; Ch'ng, E. S.; Loo, S. K.

    2015-01-01

    .05) in a microarray-profiled DLBCL dataset At the protein level examined by immunohistochemistry, HIP1R expression at 30% cut-off was associated with GCB-DLBCL molecular subtype (P = 0.0004; n = 42), and predictive of OS (P = 0.0006) and PFS (P = 0.0230) in de novo DLBCL patients treated with R-CHOP (n = 73). Cases......Huntingtin-interacting protein 1-related (HIP1R) is an endocytic protein involved in receptor trafficking, including regulating cell surface expression of receptor tyrosine kinases. We have previously shown that low HIP1R protein expression was associated with poorer survival in diffuse large B...... with high FOXP1 and low HIP1R expression frequency (FOXP1(hi)/HIP1R(lo) phenotype) exhibited poorer OS (P = 0.0038) and PFS (P = 0.0134). Multivariate analysis showed that HIP1R...

  2. Mixed compared with single-source proteins in high-protein diets affect kidney structure and function differentially in obese fa/fa Zucker rats.

    Science.gov (United States)

    Devassy, Jessay G; Wojcik, Jennifer L; Ibrahim, Naser H M; Zahradka, Peter; Taylor, Carla G; Aukema, Harold M

    2017-02-01

    Questions remain regarding the potential negative effects of dietary high protein (HP) on kidney health, particularly in the context of obesity in which the risk for renal disease is already increased. To examine whether some of the variability in HP effects on kidney health may be due to source of protein, obese fa/fa Zucker rats were given HP (35% of energy from protein) diets containing either casein, soy protein, or a mixed source of animal and plant proteins for 12 weeks. Control lean and obese rats were given diets containing casein at normal protein (15% of energy from protein) levels. Body weight and blood pressure were measured, and markers of renal structural changes, damage, and function were assessed. Obesity alone resulted in mild renal changes, as evidenced by higher kidney weights, proteinuria, and glomerular volumes. In obese rats, increasing the protein level using the single, but not mixed, protein sources resulted in higher renal fibrosis compared with the lean rats. The mixed-protein HP group also had lower levels of serum monocyte chemoattractant protein-1, even though this diet further increased kidney and glomerular size. Soy and mixed-protein HP diets also resulted in a small number of damaged glomeruli, while soy compared with mixed-protein HP diet delayed the increase in blood pressure over time. Since obesity itself confers added risk of renal disease, an HP diet from mixed-protein sources that enables weight loss but has fewer risks to renal health may be advantageous.

  3. The vacuolar protein sorting genes in insects: A comparative genome view.

    Science.gov (United States)

    Li, Zhaofei; Blissard, Gary

    2015-07-01

    In eukaryotic cells, regulated vesicular trafficking is critical for directing protein transport and for recycling and degradation of membrane lipids and proteins. Through carefully regulated transport vesicles, the endomembrane system performs a large and important array of dynamic cellular functions while maintaining the integrity of the cellular membrane system. Genetic studies in yeast Saccharomyces cerevisiae have identified approximately 50 vacuolar protein sorting (VPS) genes involved in vesicle trafficking, and most of these genes are also characterized in mammals. The VPS proteins form distinct functional complexes, which include complexes known as ESCRT, retromer, CORVET, HOPS, GARP, and PI3K-III. Little is known about the orthologs of VPS proteins in insects. Here, with the newly annotated Manduca sexta genome, we carried out genomic comparative analysis of VPS proteins in yeast, humans, and 13 sequenced insect genomes representing the Orders Hymenoptera, Diptera, Hemiptera, Phthiraptera, Lepidoptera, and Coleoptera. Amino acid sequence alignments and domain/motif structure analyses reveal that most of the components of ESCRT, retromer, CORVET, HOPS, GARP, and PI3K-III are evolutionarily conserved across yeast, insects, and humans. However, in contrast to the VPS gene expansions observed in the human genome, only four VPS genes (VPS13, VPS16, VPS33, and VPS37) were expanded in the six insect Orders. Additionally, VPS2 was expanded only in species from Phthiraptera, Lepidoptera, and Coleoptera. These studies provide a baseline for understanding the evolution of vesicular trafficking across yeast, insect, and human genomes, and also provide a basis for further addressing specific functional roles of VPS proteins in insects. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Comparative stability of canine and feline hemostatic proteins in freeze-thaw-cycled fresh frozen plasma.

    Science.gov (United States)

    Yaxley, Page E; Beal, Matthew W; Jutkowitz, L Ari; Hauptman, Joe G; Brooks, Marjory B; Hale, Anne S; Parr, Alice

    2010-10-01

    To evaluate the stability of canine and feline hemostatic proteins in freeze-thaw-cycled (FTC) fresh frozen plasma (FFP). Prospective study. Veterinary Teaching Hospital. Nine blood donor dogs and 10 blood donor cats. Whole blood was collected and separated into packed RBC and plasma units according to standard methods. Each unit of plasma was divided into 2 equal aliquots and frozen (-41 °C). One aliquot from each donor (FTC) was then thawed and then refrozen (-41 °C) until time of analysis. The second aliquot (nonfreeze-thaw-cycled; NFTC) remained frozen until time of analysis. The hemostatic proteins assessed included coagulation factors, anticoagulant factors (antithrombin and Protein C), and adhesive proteins (fibrinogen and von Willebrand Factor). The coagulant activities of factors II, VII, VIII, IX, X, XI, and XII were measured in modified one-stage activated partial thromboplastin time or prothrombin time assays. Antithrombin and Protein C activities were measured in chromogenic substrate assays. Clottable fibrinogen was measured via the Clauss method, and von Willebrand Factor concentration (vWF:Ag) was measured in an ELISA. A paired t-test was utilized to identify differences in factor activity or concentration between FTC FFP and NFTC FFP. No clinically or statistically significant differences (all P>0.05) were identified between FTC FFP and NFTC FFP. Refreezing FFP within 1 hour of initial thawing appeared to have no deleterious effects on the hemostatic protein activity or content of that unit. Transfusion of FTC FFP is expected to provide the recipient with comparable replacement of hemostatic proteins as FFP that has remained frozen. © Veterinary Emergency and Critical Care Society 2010.

  5. Comparative genome analysis reveals a conserved family of actin-like proteins in apicomplexan parasites

    Directory of Open Access Journals (Sweden)

    Sibley L David

    2005-12-01

    Full Text Available Abstract Background The phylum Apicomplexa is an early-branching eukaryotic lineage that contains a number of important human and animal pathogens. Their complex life cycles and unique cytoskeletal features distinguish them from other model eukaryotes. Apicomplexans rely on actin-based motility for cell invasion, yet the regulation of this system remains largely unknown. Consequently, we focused our efforts on identifying actin-related proteins in the recently completed genomes of Toxoplasma gondii, Plasmodium spp., Cryptosporidium spp., and Theileria spp. Results Comparative genomic and phylogenetic studies of apicomplexan genomes reveals that most contain only a single conventional actin and yet they each have 8–10 additional actin-related proteins. Among these are a highly conserved Arp1 protein (likely part of a conserved dynactin complex, and Arp4 and Arp6 homologues (subunits of the chromatin-remodeling machinery. In contrast, apicomplexans lack canonical Arp2 or Arp3 proteins, suggesting they lost the Arp2/3 actin polymerization complex on their evolutionary path towards intracellular parasitism. Seven of these actin-like proteins (ALPs are novel to apicomplexans. They show no phylogenetic associations to the known Arp groups and likely serve functions specific to this important group of intracellular parasites. Conclusion The large diversity of actin-like proteins in apicomplexans suggests that the actin protein family has diverged to fulfill various roles in the unique biology of intracellular parasites. Conserved Arps likely participate in vesicular transport and gene expression, while apicomplexan-specific ALPs may control unique biological traits such as actin-based gliding motility.

  6. A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi.

    Science.gov (United States)

    Sperschneider, Jana; Gardiner, Donald M; Taylor, Jennifer M; Hane, James K; Singh, Karam B; Manners, John M

    2013-11-20

    Fungal pathogens cause devastating losses in economically important cereal crops by utilising pathogen proteins to infect host plants. Secreted pathogen proteins are referred to as effectors and have thus far been identified by selecting small, cysteine-rich peptides from the secretome despite increasing evidence that not all effectors share these attributes. We take advantage of the availability of sequenced fungal genomes and present an unbiased method for finding putative pathogen proteins and secreted effectors in a query genome via comparative hidden Markov model analyses followed by unsupervised protein clustering. Our method returns experimentally validated fungal effectors in Stagonospora nodorum and Fusarium oxysporum as well as the N-terminal Y/F/WxC-motif from the barley powdery mildew pathogen. Application to the cereal pathogen Fusarium graminearum reveals a secreted phosphorylcholine phosphatase that is characteristic of hemibiotrophic and necrotrophic cereal pathogens and shares an ancient selection process with bacterial plant pathogens. Three F. graminearum protein clusters are found with an enriched secretion signal. One of these putative effector clusters contains proteins that share a [SG]-P-C-[KR]-P sequence motif in the N-terminal and show features not commonly associated with fungal effectors. This motif is conserved in secreted pathogenic Fusarium proteins and a prime candidate for functional testing. Our pipeline has successfully uncovered conservation patterns, putative effectors and motifs of fungal pathogens that would have been overlooked by existing approaches that identify effectors as small, secreted, cysteine-rich peptides. It can be applied to any pathogenic proteome data, such as microbial pathogen data of plants and other organisms.

  7. Role of Cell Cycle Regulation and MLH1, A Key DNA Mismatch Repair Protein, In Adaptive Survival Responses. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    David A. Boothman

    1999-08-11

    Due to several interesting findings on both adaptive survival responses (ASRs) and DNA mismatch repair (MMR), this grant was separated into two discrete Specific Aim sets (each with their own discrete hypotheses). The described experiments were simultaneously performed.

  8. AB Initio Protein Tertiary Structure Prediction: Comparative-Genetic Algorithm with Graph Theoretical Methods

    Energy Technology Data Exchange (ETDEWEB)

    Gregurick, S. K.

    2001-04-20

    During the period from September 1, 1998 until September 1, 2000 I was awarded a Sloan/DOE postdoctoral fellowship to work in collaboration with Professor John Moult at the Center for Advanced Research in Biotechnology (CARB). Our research project, ''Ab Initio Protein Tertiary Structure Prediction and a Comparative Genetic algorithm'', yielded promising initial results. In short, the project is designed to predict the native fold, or native tertiary structure, of a given protein by inputting only the primary sequence of the protein (one or three letter code). The algorithm is based on a general learning, or evolutionary algorithm and is called Genetic Algorithm (GAS). In our particular application of GAS, we search for native folds, or lowest energy structures, using two different descriptions for the interactions of the atoms and residues in a given protein sequence. One potential energy function is based on a free energy description, while the other function is a threading potential derived by Moult and Samudrala. This modified genetic algorithm was loosely termed a Comparative Genetic Algorithm and was designed to search for native folded structures on both potential energy surfaces, simultaneously. We tested the algorithm on a series of peptides ranging from 11 to 15 residues in length, which are thought to be independent folding units and thereby will fold to native structures independent of the larger protein environment. Our initial results indicated a modest increase in accuracy, as compared to a standard Genetic Algorithm. We are now in the process of improving the algorithm to increase the sensitivity to other inputs, such as secondary structure requirements. The project did not involve additional students and as of yet, the work has not been published.

  9. Actin, actin-related proteins and profilin in diatoms: a comparative genomic analysis.

    Science.gov (United States)

    Aumeier, Charlotte; Polinski, Ellen; Menzel, Diedrik

    2015-10-01

    Diatoms are heterokont unicellular algae with a widespread distribution throughout all aquatic habitats. Research on diatoms has advanced significantly over the last decade due to available genetic transformation methods and publicly available genome databases. Yet up to now, proteins involved in the regulation of the cytoskeleton in diatoms are largely unknown. Consequently, this work focuses on actin and actin-related proteins (ARPs) encoded in the diatom genomes of Thalassiosira pseudonana, Thalassiosira oceanica, Phaeodactylum tricornutum, Fragilariopsis cylindrus and Pseudo-nitzschia multiseries. Our comparative genomic study revealed that most diatoms possess only a single conventional actin and a small set of ARPs. Among these are the highly conserved cytoplasmic Arp1 protein and the nuclear Arp4 as well as Arp6. Diatom genomes contain genes coding for two structurally different homologues of Arp4 that might serve specific functions. All diatom species examined here lack ARP2 and ARP3 proteins, suggesting that diatoms are not capable of forming the Arp2/3 complex, which is essential in most eukaryotes for actin filament branching and plus-end dynamics. Interestingly, none of the sequenced representatives of the Bacillariophyta phylum code for profilin. Profilin is an essential actin-binding protein regulating the monomer actin pool and is involved in filament plus-end dynamics. This is the first report of organisms not containing profilin. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Proteomics identifies differentially expressed proteins in neonatal murine thymus compared with adults

    Directory of Open Access Journals (Sweden)

    Cai Xinze

    2012-11-01

    Full Text Available Abstract Background The thymus is an immune organ essential for life and plays a crucial role in the development of T cells. It undergoes a fetal to adult developmental maturation process occurring in mouse during the postnatal months. The molecular modifications underlying these ontogenic changes are essentially unknown. Here we used a differential proteomic-based technique (2D-Difference Gel Electrophoresis coupled with matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF mass spectrometry to search for key proteins in the postnatal development of the thymus. Eight different BALB/c mice were used in the study: four mice aged of 1 day (neonatal and four mice aged of 60 days (adult. Protein samples derived from thymus were labeled and run in 2D-PAGE (Two-Dimensional Polyacrylamide Gel Electrophoresis. One whole-thymus tissue from each mouse was run on gels and each gel containing a pooled sample of the eight mice was run in parallel. The pooled sample was set as the internal pool, containing equal amount of each protein extract used in the experiment. Gels were matched and compared with Difference In-gel Analysis software. Differential spots were picked, in-gel digested and peptide mass fingerprints were obtained. Results Among the differentially regulated proteins in neonatal thymus group, 111 proteins were identified by mass spectrometry, of which 95 proteins were up-regulated and 16 proteins were down-regulated. The identified proteins belong to several functional categories, including cell proliferation, cycle and apoptosis, transcription regulation, signal transduction, nucleotide processing, proteolysis and translation, protein folding, metabolism, oxidoreduction, cytoskeleton, immune response, and embryonic development. The major interaction networks comprised of cellular function and maintenance, cellular assembly and organization, and metabolism were also identified by STRING analysis. Conclusions The demonstrated

  11. Simultaneous cytoplasmic and nuclear protein expression of melanoma antigen-A family and NY-ESO-1 cancer-testis antigens represents an independent marker for poor survival in head and neck cancer.

    Science.gov (United States)

    Laban, Simon; Atanackovic, Djordje; Luetkens, Tim; Knecht, Rainald; Busch, Chia-Jung; Freytag, Marcus; Spagnoli, Giulio; Ritter, Gerd; Hoffmann, Thomas K; Knuth, Alexander; Sauter, Guido; Wilczak, Waldemar; Blessmann, Marco; Borgmann, Kerstin; Muenscher, Adrian; Clauditz, Till S

    2014-09-01

    The prognosis of head and neck squamous cell carcinoma (HNSCC) patients remains poor. The identification of high-risk subgroups is needed for the development of custom-tailored therapies. The expression of cancer-testis antigens (CTAs) has been linked to a worse prognosis in other cancer types; however, their prognostic value in HNSCC is unclear because only few patients have been examined and data on CTA protein expression are sparse. A tissue microarray consisting of tumor samples from 453 HNSCC patients was evaluated for the expression of CTA proteins using immunohistochemistry. Frequency of expression and the subcellular expression pattern (nuclear, cytoplasmic, or both) was recorded. Protein expression of melanoma antigen (MAGE)-A family CTA, MAGE-C family CTA and NY-ESO-1 was found in approximately 30, 7 and 4% of tumors, respectively. The subcellular expression pattern in particular had a marked impact on the patients' prognosis. Median overall survival (OS) of patients with (i) simultaneous cytoplasmic and nuclear expression compared to (ii) either cytoplasmic or nuclear expression and (iii) negative patients was 23.0 versus 109.0 versus 102.5 months, for pan-MAGE (p < 0.0001), 46.6 versus 50.0 versus 109.0 for MAGE-A3/A4 (p = 0.0074) and 13.3 versus 50.0 versus 100.2 months for NY-ESO-1 (p = 0.0019). By multivariate analysis, these factors were confirmed as independent markers for poor survival. HNSCC patients showing protein expression of MAGE-A family members or NY-ESO-1 represent a subgroup with an extraordinarily poor survival. The development of immunotherapeutic strategies targeting these CTA may, therefore, be a promising approach to improve the outcome of HNSCC patients. © 2014 UICC.

  12. Extraction of protein interaction data: a comparative analysis of methods in use.

    Science.gov (United States)

    Jose, Hena; Vadivukarasi, Thangavel; Devakumar, Jyothi

    2007-01-01

    Several natural language processing tools, both commercial and freely available, are used to extract protein interactions from publications. Methods used by these tools include pattern matching to dynamic programming with individual recall and precision rates. A methodical survey of these tools, keeping in mind the minimum interaction information a researcher would need, in comparison to manual analysis has not been carried out. We compared data generated using some of the selected NLP tools with manually curated protein interaction data (PathArt and IMaps) to comparatively determine the recall and precision rate. The rates were found to be lower than the published scores when a normalized definition for interaction is considered. Each data point captured wrongly or not picked up by the tool was analyzed. Our evaluation brings forth critical failures of NLP tools and provides pointers for the development of an ideal NLP tool.

  13. Extraction of Protein Interaction Data: A Comparative Analysis of Methods in Use

    Directory of Open Access Journals (Sweden)

    Jyothi Devakumar

    2007-12-01

    Full Text Available Several natural language processing tools, both commercial and freely available, are used to extract protein interactions from publications. Methods used by these tools include pattern matching to dynamic programming with individual recall and precision rates. A methodical survey of these tools, keeping in mind the minimum interaction information a researcher would need, in comparison to manual analysis has not been carried out. We compared data generated using some of the selected NLP tools with manually curated protein interaction data (PathArt and IMaps to comparatively determine the recall and precision rate. The rates were found to be lower than the published scores when a normalized definition for interaction is considered. Each data point captured wrongly or not picked up by the tool was analyzed. Our evaluation brings forth critical failures of NLP tools and provides pointers for the development of an ideal NLP tool.

  14. Extraction of Protein Interaction Data: A Comparative Analysis of Methods in Use

    Directory of Open Access Journals (Sweden)

    Jose Hena

    2007-01-01

    Full Text Available Several natural language processing tools, both commercial and freely available, are used to extract protein interactions from publications. Methods used by these tools include pattern matching to dynamic programming with individual recall and precision rates. A methodical survey of these tools, keeping in mind the minimum interaction information a researcher would need, in comparison to manual analysis has not been carried out. We compared data generated using some of the selected NLP tools with manually curated protein interaction data (PathArt and IMaps to comparatively determine the recall and precision rate. The rates were found to be lower than the published scores when a normalized definition for interaction is considered. Each data point captured wrongly or not picked up by the tool was analyzed. Our evaluation brings forth critical failures of NLP tools and provides pointers for the development of an ideal NLP tool.

  15. Extraction of Protein Interaction Data: A Comparative Analysis of Methods in Use

    OpenAIRE

    Jyothi Devakumar; Thangavel Vadivukarasi; Hena Jose

    2007-01-01

    Several natural language processing tools, both commercial and freely available, are used to extract protein interactions from publications. Methods used by these tools include pattern matching to dynamic programming with individual recall and precision rates. A methodical survey of these tools, keeping in mind the minimum interaction information a researcher would need, in comparison to manual analysis has not been carried out. We compared data generated using some of the selected NLP tools...

  16. Inhibition of Protein Synthesis on the Ribosome by Tildipirosin Compared with Other Veterinary Macrolides

    OpenAIRE

    Andersen, Niels Møller; Poehlsgaard, Jacob; Warrass, Ralf; Douthwaite, Stephen

    2012-01-01

    Tildipirosin is a 16-membered-ring macrolide developed to treat bacterial pathogens, including Mannheimia haemolytica and Pasteurella multocida, that cause respiratory tract infections in cattle and swine. Here we evaluated the efficacy of tildipirosin at inhibiting protein synthesis on the ribosome (50% inhibitory concentration [IC50], 0.23 ± 0.01 μM) and compared it with the established veterinary macrolides tylosin, tilmicosin, and tulathromycin. Mutation and methylation at key rRNA nucleo...

  17. Comparing the environmental impacts of alternative protein crops in poultry diets: The consequences of uncertainty

    OpenAIRE

    Leinonen, Ilkka; Adrian G Williams; Waller, Anthony H.; Kyriazakis, Ilias

    2013-01-01

    The statistical significance of the effects of including different protein sources in poultry diets on the environmental impacts Global Warming Potential (GWP), Eutrophication Potential (EP) and Acidification Potential (AP) of typical UK broiler meat and egg production systems was quantified using the Life Cycle Assessment (LCA) method combined with an uncertainty analysis. The broiler and layer diets compared in the study were either standard soya-based, or alternative diets based on Europea...

  18. Melanoma patients with unknown primary site or nodal recurrence after initial diagnosis have a favourable survival compared to those with synchronous lymph node metastasis and primary tumour.

    Directory of Open Access Journals (Sweden)

    Benjamin Weide

    Full Text Available BACKGROUND: A direct comparison of prognosis between patients with regional lymph node metastases (LNM detected synchronously with the primary melanoma (primary LNM, patients who developed their first LNM subsequently (secondary LNM and those with initial LNM in melanoma with unknown primary site (MUP is missing thus far. PATIENTS AND METHODS: Survival of 498 patients was calculated from the time point of the first macroscopic LNM using Kaplan Meier and multivariate Cox hazard regression analysis. RESULTS: Patients with secondary LNM (HR = 0.67; p = 0.009 and those with initial LNM in MUP (HR = 0.45; p = 0.008 had a better prognosis compared to patients with primary LNM (median survival time 52 and 65 vs. 24 months, respectively. A high number of involved nodes, the presence of in-transit/satellite metastases and male gender had an additional independent unfavourable effect. CONCLUSIONS: Survival of patients with LNM in MUP and with secondary LNM is similar and considerably more favourable compared to those with primary LNM. This difference needs to be considered during patient counselling and for stratification purposes in clinical trials. The assumption of an immune privilege of patients with MUP which is responsible for rejection of the primary melanoma, and results in a favourable prognosis is not supported by our data.

  19. Bone protein “extractomics”: comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics

    Directory of Open Access Journals (Sweden)

    Elena R. Schroeter

    2016-10-01

    Full Text Available Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous

  20. Bone protein "extractomics": comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics.

    Science.gov (United States)

    Schroeter, Elena R; DeHart, Caroline J; Schweitzer, Mary H; Thomas, Paul M; Kelleher, Neil L

    2016-01-01

    Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different "extractomes" will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these

  1. Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species.

    Science.gov (United States)

    Trost, Matthias; Wehmhöner, Dirk; Kärst, Uwe; Dieterich, Guido; Wehland, Jürgen; Jänsch, Lothar

    2005-04-01

    Extracellular proteins of bacterial pathogens play a crucial role in the infection of the host. Here we present the first comprehensive validation of the secretory subproteome of the Gram positive pathogen Listeria monocytogenes using predictive bioinformatic and experimental proteomic approaches. The previous original signal peptide (SP) prediction (Glaser et al., Science 2001, 294, 849-852) has been greatly improved by an in-depth analysis using seven different bioinformatic tools. Subsequent careful classification of the resulting data gives a probability dependent annotation of 121 putatively secreted proteins of which 45 are novel. Complementary proteomic analysis using both two-dimensional gel electrophoresis/matrix assisted laser desorption/ionization mass spectrometry and high performance liquid chromatography/electrospray ionization-mass spectrometry has identified 105 proteins in the culture supernatant of L. monocytogenes. Among these, we were able to detect all the currently known virulence factors with an SP showing the importance of this subproteome and demonstrating the reliability of the techniques used. The comparison between the L. monocytogenes wildtype and the nonpathogenic species Listeria innocua was performed to reveal proteins probably involved in pathogenicity and/or the adaptation to their respective lifestyles. In addition to the eight known virulence factors, all of which have no orthologous genes in L. innocua, eight additional proteins have been identified that exhibit the typical key feature defining the known listerial virulence factors. Further significant differences between the two species are evident in the group of cell wall and secretory proteins that warrant further study. Our investigation clearly demonstrates that the major difference between the pathogenic and nonpathogenic species, noted in the comparative genome analysis, manifests itself strongest in the secretome.

  2. Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins.

    Science.gov (United States)

    Staats, Charley Christian; Junges, Angela; Guedes, Rafael Lucas Muniz; Thompson, Claudia Elizabeth; de Morais, Guilherme Loss; Boldo, Juliano Tomazzoni; de Almeida, Luiz Gonzaga Paula; Andreis, Fábio Carrer; Gerber, Alexandra Lehmkuhl; Sbaraini, Nicolau; da Paixão, Rana Louise de Andrade; Broetto, Leonardo; Landell, Melissa; Santi, Lucélia; Beys-da-Silva, Walter Orlando; Silveira, Carolina Pereira; Serrano, Thaiane Rispoli; de Oliveira, Eder Silva; Kmetzsch, Lívia; Vainstein, Marilene Henning; de Vasconcelos, Ana Tereza Ribeiro; Schrank, Augusto

    2014-09-29

    Metarhizium anisopliae is an entomopathogenic fungus used in the biological control of some agricultural insect pests, and efforts are underway to use this fungus in the control of insect-borne human diseases. A large repertoire of proteins must be secreted by M. anisopliae to cope with the various available nutrients as this fungus switches through different lifestyles, i.e., from a saprophytic, to an infectious, to a plant endophytic stage. To further evaluate the predicted secretome of M. anisopliae, we employed genomic and transcriptomic analyses, coupled with phylogenomic analysis, focusing on the identification and characterization of secreted proteins. We determined the M. anisopliae E6 genome sequence and compared this sequence to other entomopathogenic fungi genomes. A robust pipeline was generated to evaluate the predicted secretomes of M. anisopliae and 15 other filamentous fungi, leading to the identification of a core of secreted proteins. Transcriptomic analysis using the tick Rhipicephalus microplus cuticle as an infection model during two periods of infection (48 and 144 h) allowed the identification of several differentially expressed genes. This analysis concluded that a large proportion of the predicted secretome coding genes contained altered transcript levels in the conditions analyzed in this study. In addition, some specific secreted proteins from Metarhizium have an evolutionary history similar to orthologs found in Beauveria/Cordyceps. This similarity suggests that a set of secreted proteins has evolved to participate in entomopathogenicity. The data presented represents an important step to the characterization of the role of secreted proteins in the virulence and pathogenicity of M. anisopliae.

  3. Comparable Survival between Additional Radiotherapy and Local Surgery in Occult Breast Cancer after Axillary Lymph Node Dissection: A Population-based Analysis.

    Science.gov (United States)

    Wu, San-Gang; Zhang, Wen-Wen; Sun, Jia-Yuan; Li, Feng-Yan; Lin, Huan-Xin; Chen, Yong-Xiong; He, Zhen-Yu

    2017-01-01

    Purpose: To investigate the clinical value of additional local treatment strategies in occult breast cancer (OBC) after axillary lymph node dissection (ALND). Methods: Patients diagnosed with OBC between 1990 and 2013 were included from the Surveillance, Epidemiology, and End Results registry database. The significant risk factors of cause-specific survival (CSS) and overall survival (OS) were identified using univariate and multivariate Cox regression analyses. Results: We identified 980 patients, including 219 (22.3%), 252 (25.7%), 263 (26.8%), and 246 (25.1%) of patients underwent ALND, ALND + radiotherapy (RT), ALND + surgery (S) (mastectomy or breast-conserving surgery), and ALND + S + RT, respectively. Patients with younger age, diagnosed before 2000, advanced nodal stage, ER-negative disease, and PR-negative disease were more likely to undergo additional local treatment compared with ALND only. The 10-year rate CSS of the ALND only group was 57.2%, while that of the ALND + RT, ALND + S, and ALND + S + RT groups was 78.0%, 81.0%, and 71.5%, respectively (p analysis indicated that older age, advanced nodal stage, and ALND only were independent risk factors for decreased CSS and OS. CSS and OS among the groups including ALND + RT, ALND + S, and ALND + S + RT were not significantly different. Conclusions: Additional local treatment (local surgery or RT) improves survival outcomes compared with ALND only in OBC after ALND. ALND + RT may be the optimal local treatment for OBC due to no different in survival outcomes and cosmesis is better.

  4. Multicenter, phase III trial comparing selenium supplementation with observation in gynecologic radiation oncology: follow-up analysis of the survival data 6 years after cessation of randomization.

    Science.gov (United States)

    Muecke, Ralph; Micke, Oliver; Schomburg, Lutz; Glatzel, Michael; Reichl, Berthold; Kisters, Klaus; Schaefer, Ulrich; Huebner, Jutta; Eich, Hans T; Fakhrian, K; Adamietz, Irenaeus A; Buentzel, Jens

    2014-11-01

    In 2010, we reported that selenium (Se) supplementation during radiation therapy (RT) is effective for increasing blood Se levels in Se-deficient cervical and uterine cancer patients, and reduced the number of episodes and severity of RT-induced diarrhea. In the current study, we examine whether of Se supplementation during adjuvant RT affects long-term survival of these patients. Former patients were identified and questioned with respect to their health and well-being. A total of 81 patients were randomized in the initial supplementation study, 39 of whom received Se (selenium group, SeG) and 42 of whom served as controls (control group, CG). When former patients were reidentified after a median follow-up of 70 months (range = 0-136), the actuarial 10-year disease-free survival rate in the SeG was 80.1% compared to 83.2% in the CG (P = .65), and the actuarial 10-year overall survival rate of patients in the SeG was 55.3% compared to 42.7% in the CG (P = .09). Our extended follow-up analysis demonstrates that Se supplementation had no influence on the effectiveness of the anticancer irradiation therapy and did not negatively affect patients' long-term survival. In view of its positive effects on RT-induced diarrhea, we consider Se supplementation to be a meaningful and beneficial adjuvant treatment in Se-deficient cervical and uterine cancer patients while undergoing pelvic radiation therapy. © The Author(s) 2014.

  5. Expression, purification, crystallization and preliminary X-ray characterization of two crystal forms of stationary-phase survival E protein from Campylobacter jejuni

    Energy Technology Data Exchange (ETDEWEB)

    Gonçalves, A. M. D.; Rêgo, A. T. [Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras (Portugal); Thomaz, M. [Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras (Portugal); Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2748-901 Oeiras (Portugal); Enguita, F. J., E-mail: fenguita@fm.ul.pt [Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras (Portugal); Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa (Portugal); Carrondo, M. A. [Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras (Portugal)

    2008-03-01

    Survival E (SurE) protein from Campylobacter jejuni, a Gram-negative mesophile, has been overexpressed in Escherichia coli as a soluble protein, successfully purified and crystallized in two distinct crystal forms. Survival E (SurE) protein from Campylobacter jejuni, a Gram-negative mesophile, has been overexpressed in Escherichia coli as a soluble protein, successfully purified and crystallized in two distinct crystal forms. The first form belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with a tetramer in the asymmetric unit and unit-cell parameters a = 80.5, b = 119.0, c = 135.3 Å. The second form belongs to space group C2, with unit-cell parameters a = 121.4, b = 47.1, c = 97.8 Å, and contains a dimer in the asymmetric unit. Diffraction data have been collected from these crystal forms to 2.5 and 2.95 Å resolution, respectively.

  6. Comparative analyses of transport proteins encoded within the genomes of Leptospira species.

    Science.gov (United States)

    Buyuktimkin, Bora; Saier, Milton H

    2016-09-01

    Select species of the bacterial genus Leptospira are causative agents of leptospirosis, an emerging global zoonosis affecting nearly one million people worldwide annually. We examined two Leptospira pathogens, Leptospira interrogans serovar Lai str. 56601 and Leptospira borgpetersenii serovar Hardjo-bovis str. L550, as well as the free-living leptospiral saprophyte, Leptospira biflexa serovar Patoc str. 'Patoc 1 (Ames)'. The transport proteins of these leptospires were identified and compared using bioinformatics to gain an appreciation for which proteins may be related to pathogenesis and saprophytism. L. biflexa possesses a disproportionately high number of secondary carriers for metabolite uptake and environmental adaptability as well as an increased number of inorganic cation transporters providing ionic homeostasis and effective osmoregulation in a rapidly changing environment. L. interrogans and L. borgpetersenii possess far fewer transporters, but those that they all have are remarkably similar, with near-equivalent representation in most transporter families. These two Leptospira pathogens also possess intact sphingomyelinases, holins, and virulence-related outer membrane porins. These virulence-related factors, in conjunction with decreased transporter substrate versatility, indicate that pathogenicity arose in Leptospira correlating to progressively narrowing ecological niches and the emergence of a limited set of proteins responsible for host invasion. The variability of host tropism and mortality rates by infectious leptospires suggests that small differences in individual sets of proteins play important physiological and pathological roles. Copyright © 2016. Published by Elsevier Ltd.

  7. Comparative genomic analyses of transport proteins encoded within the genomes of Leptospira species.

    Science.gov (United States)

    Buyuktimkin, Bora; Saier, Milton H

    2015-11-01

    Select species of the bacterial genus Leptospira are causative agents of leptospirosis, an emerging global zoonosis affecting nearly one million people worldwide annually. We examined two Leptospira pathogens, Leptospira interrogans serovar Lai str. 56601 and Leptospira borgpetersenii serovar Hardjo-bovis str. L550, as well as the free-living leptospiral saprophyte, Leptospira biflexa serovar Patoc str. 'Patoc 1 (Ames)'. The transport proteins of these leptospires were identified and compared using bioinformatics to gain an appreciation for which proteins may be related to pathogenesis and saprophytism. L. biflexa possesses a disproportionately high number of secondary carriers for metabolite uptake and environmental adaptability as well as an increased number of inorganic cation transporters providing ionic homeostasis and effective osmoregulation in a rapidly changing environment. L. interrogans and L. borgpetersenii possess far fewer transporters, but those that they have are remarkably similar, with near-equivalent representation in most transporter families. These two Leptospira pathogens also possess intact sphingomyelinases, holins, and virulence-related outer membrane porins. These virulence-related factors, in conjunction with decreased transporter substrate versatility, indicate that pathogenicity was accompanied by progressively narrowing ecological niches and the emergence of a limited set of proteins responsible for host invasion. The variability of host tropism and mortality rates by infectious leptospires suggests that small differences in individual sets of proteins play important physiological and pathological roles. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. A comparative study of the retention and lethality of the first and second generation arthropod protein markers

    Science.gov (United States)

    A greenhouse study was conducted that compared the protein mark retention time of a well established rabbit IgG protein detection protocol with those of three newer, less expensive protein detection protocols designed to detect casein in bovine milk, egg albumin in chicken egg whites, and soy tryp...

  9. A Comparative Study of Defibrillator Leads at a Large-Volume Implanting Hospital: Results From the Pacemaker and Implantable Defibrillator Leads Survival Study ("PAIDLESS").

    Science.gov (United States)

    Cohen, Todd J; Asheld, Wilbur J; Germano, Joseph; Islam, Shahidul; Patel, Dhimesh

    2015-06-01

    The purpose of the study was to examine survival in the implantable defibrillator subset of implanted leads at a large-volume implanting hospital. Implantable lead survival has been the subject of many multicenter studies over the past decade. Fewer large implanting volume single-hospital studies have examined defibrillator lead failure as it relates to patient survival and lead construction. This investigator-initiated retrospective study examined defibrillator lead failure in those who underwent implantation of a defibrillator between February 1, 1996 and December 31, 2011. Lead failure was defined as: failure to capture/sense, abnormal pacing and/or defibrillator impedance, visual insulation defect or lead fracture, extracardiac stimulation, cardiac perforation, tricuspid valve entrapment, lead tip fracture and/or lead dislodgment. Patient characteristics, implant approach, lead manufacturers, lead models, recalled status, patient mortality, and core lead design elements were compared using methods that include Kaplan Meier analysis, univariate and multivariable Cox regression models. A total of 4078 defibrillator leads were implanted in 3802 patients (74% male; n = 2812) with a mean age of 70 ± 13 years at Winthrop University Hospital. Lead manufacturers included: Medtronic: [n = 1834; 801 recalled]; St. Jude Medical: [n = 1707; 703 recalled]; Boston Scientific: [n = 537; 0 recalled]. Kaplan-Meier analysis adjusted for multiple comparisons revealed that both Boston Scientific's and St. Jude Medical's leads had better survival than Medtronic's leads (PLead survival was comparable between Boston Scientific and St. Jude Medical (P=.80). A total of 153 leads failed (3.5% of all leads) during the study. There were 99 lead failures from Medtronic (5.4% failure rate); 56 were recalled Sprint Fidelis leads. There were 36 lead failures from St. Jude (2.1% failure rate); 20 were recalled Riata or Riata ST leads. There were 18 lead failures from Boston Scientific (3

  10. Prediction of mitochondrial protein function by comparative physiology and phylogenetic profiling.

    Science.gov (United States)

    Cheng, Yiming; Perocchi, Fabiana

    2015-01-01

    According to the endosymbiotic theory, mitochondria originate from a free-living alpha-proteobacteria that established an intracellular symbiosis with the ancestor of present-day eukaryotic cells. During the bacterium-to-organelle transformation, the proto-mitochondrial proteome has undergone a massive turnover, whereby less than 20 % of modern mitochondrial proteomes can be traced back to the bacterial ancestor. Moreover, mitochondrial proteomes from several eukaryotic organisms, for example, yeast and human, show a rather modest overlap, reflecting differences in mitochondrial physiology. Those differences may result from the combination of differential gain and loss of genes and retargeting processes among lineages. Therefore, an evolutionary signature, also called "phylogenetic profile", could be generated for every mitochondrial protein. Here, we present two evolutionary biology approaches to study mitochondrial physiology: the first strategy, which we refer to as "comparative physiology," allows the de novo identification of mitochondrial proteins involved in a physiological function; the second, known as "phylogenetic profiling," allows to predict protein functions and functional interactions by comparing phylogenetic profiles of uncharacterized and known components.

  11. Comparative evaluation of standardized ileal amino acid digestibility in protein supplements for piglets.

    Science.gov (United States)

    Eklund, M; Sauer, N; Hörner, S; Rademacher, M; Mosenthin, R

    2012-12-01

    Standardized ileal digestibility (SID) of AA was determined in 6 protein ingredients for piglets. A basal diet based on corn (Zea mays) starch and casein was supplemented with fluid-bed-dried porcine intestinal mucosa hydrolysate, spray-dried porcine intestinal mucosa hydrolysate, soy (Glycine max) protein concentrate, 2 batches of soy protein, or full-fat soybeans. The SID of AA did not differ between the 4 soybean products (P > 0.05). Compared to most SID values in the 4 soybean products, SID of AA were lower in the 2 porcine intestinal mucosa hydrolysates (P ≤ 0.05). In conclusion, although the initial trypsin inhibitor contents in the raw soybeans have not been determined, high SID values in the 4 soybean products indicate that the different processing procedures used to manufacture these products were efficient to inactivate trypsin inhibitors. For most AA in the 2 porcine intestinal mucosa hydrolysates, drying procedure did not affect SID of AA, but SID values were generally lower compared to the 4 soybean products.

  12. Rv0216, a Conserved Hypothetical Protein from Myocbacterium Tuberculosis that is Essential for Bacterial Survival During Infection, has a Double Hotdog Fold

    Energy Technology Data Exchange (ETDEWEB)

    Castell,A.; Johansson, P.; Unge, T.; Jones, T.; Backbro, K.

    2005-01-01

    The Mycobacterium tuberculosis genome contains about 4000 genes, of which approximately a third code for proteins of unknown function or are classified as conserved hypothetical proteins. We have determined the three-dimensional structure of one of these, the rv0216 gene product, which has been shown to be essential for M. tuberculosis growth in vivo. The structure exhibits the greatest similarity to bacterial and eukaryotic hydratases that catalyse the R-specific hydration of 2-enoyl coenzyme A. However, only part of the catalytic machinery is conserved in Rv0216 and it showed no activity for the substrate crotonyl-CoA. The structure of Rv0216 allows us to assign new functional annotations to a family of seven other M. tuberculosis proteins, a number if which are essential for bacterial survival during infection and growth.

  13. Protein kinase Cα (PKCα) regulates p53 localization and melanoma cell survival downstream of integrin αv in three-dimensional collagen and in vivo.

    Science.gov (United States)

    Smith, Stephen D; Enge, Martin; Bao, Wenjie; Thullberg, Minna; Costa, Tânia D F; Olofsson, Helene; Gashi, Behxhet; Selivanova, Galina; Strömblad, Staffan

    2012-08-24

    Protein kinase C α (PKCα) is overexpressed in numerous types of cancer. Importantly, PKCα has been linked to metastasis of malignant melanoma in patients. However, it has been unclear how PKCα may be regulated and how it exerts its role in melanoma. Here, we identified a role for PKCα in melanoma cell survival in a three-dimensional collagen model mimicking the in vivo pathophysiology of the dermis. A pathway was identified that involved integrin αv-mediated up-regulation of PKCα and PKCα-dependent regulation of p53 localization, which was connected to melanoma cell survival. Melanoma survival and growth in three-dimensional microenvironments requires the expression of integrin αv, which acts to suppress p53 activity. Interestingly, microarray analysis revealed that PKCα was up-regulated by integrin αv in a three-dimensional microenvironment-dependent manner. Integrin αv was observed to promote a relocalization of endogenous p53 from the nucleus to the cytoplasm upon growth in three-dimensional collagen as well as in vivo, whereas stable knockdown of PKCα inhibited the integrin αv-mediated relocalization of p53. Importantly, knockdown of PKCα also promoted apoptosis in three-dimensional collagen and in vivo, resulting in reduced tumor growth. This indicates that PKCα constitutes a crucial component of the integrin αv-mediated pathway(s) that promote p53 relocalization and melanoma survival.

  14. Microencapsulation of Lactobacillus rhamnosus GG by Transglutaminase Cross-Linked Soy Protein Isolate to Improve Survival in Simulated Gastrointestinal Conditions and Yoghurt.

    Science.gov (United States)

    Li, Chun; Wang, Chun-Ling; Sun, Yu; Li, Ai-Li; Liu, Fei; Meng, Xiang-Chen

    2016-07-01

    Microencapsulation is an effective way to improve the survival of probiotics in simulated gastrointestinal (GI) conditions and yoghurt. In this study, microencapsulation of Lactobacillus rhamnosus GG (LGG) was prepared by first cross-linking of soy protein isolate (SPI) using transglutaminase (TGase), followed by embedding the bacteria in cross-linked SPI, and then freeze-drying. The survival of microencapsulated LGG was evaluated in simulated GI conditions and yoghurt. The results showed that a high microencapsulation yield of 67.4% was obtained. The diameter of the microencapsulated LGG was in the range of 52.83 to 275.16 μm. Water activity did not differ between free and microencapsulated LGG after freeze-drying. The survival of microencapsulated LGG under simulated gastric juice (pH 2.5 and 3.6), intestinal juice (0.3% and 2% bile salt) and storage at 4 °C were significantly higher than that of free cells. The survival of LGG in TGase cross-linked SPI microcapsules was also improved to 14.5 ± 0.5% during storage in yoghurt. The microencapsulation of probiotics by TGase-treated SPI can be a suitable alternative to polysaccharide gelation technologies. © 2016 Institute of Food Technologists®

  15. Comparative Growth and Survival of Hylurgus ligniperda (Coleoptera: Scolytinae) and Arhopalus ferus (Coleoptera: Cerambycidae) Reared on Artificial or Natural Diet at 15 or 25°C.

    Science.gov (United States)

    Romo, C M; Bader, M K-F; Pawson, S M

    2016-02-01

    Two saproxylic forest insects, Hylurgus ligniperda (F.) (Coleoptera: Scolytinae) and Arhopalus ferus (Mulsant)(Coleoptera: Cerambycidae), were reared on artificial or natural diet at 15 or 25°C to compare larval growth rates and survival. A significant diet by temperature interaction was observed in the growth of H. ligniperda larvae,which developed faster when reared on natural diet at 15°C, but grew faster and pupated significantly earlier when reared on artificial diet at 25°C. However, H. ligniperda survival by the end of the experiment was low on both diets when reared at 25°C (10.1%, 95% CI: 5.2–15.1%), which suggests that rearing at lower temperatures may be required. A. ferus larvae gained significantly larger body size when reared on artificial diet than on natural diet at both temperatures. Survival of A. ferus reared on artificial diet was significantly lower than larvae reared on natural diet at 25°C. The significant differences between A. ferus larval development rates when reared on artificial and natural diets preclude the use of artificial diet to collect meaningful data to construct temperature development models for ecological comparisons. Artificial diet provided a suitable medium for mass production of individuals for research purposes, e.g., test mortality in response to treatments. However, additional rearing studies are needed to determine whether the larger artificially reared larvae result in adults that are healthier, more productive, and live longer.

  16. Introducing Students to Protein Analysis Techniques: Separation and Comparative Analysis of Gluten Proteins in Various Wheat Strains

    Science.gov (United States)

    Pirinelli, Alyssa L.; Trinidad, Jonathan C.; Pohl, Nicola L. B.

    2016-01-01

    Polyacrylamide gel electrophoresis (PAGE) is commonly taught in undergraduate laboratory classes as a traditional method to analyze proteins. An experiment has been developed to teach these basic protein gel skills in the context of gluten protein isolation from various types of wheat flour. A further goal is to relate this technique to current…

  17. SiteBinder: an improved approach for comparing multiple protein structural motifs.

    Science.gov (United States)

    Sehnal, David; Vařeková, Radka Svobodová; Huber, Heinrich J; Geidl, Stanislav; Ionescu, Crina-Maria; Wimmerová, Michaela; Koča, Jaroslav

    2012-02-27

    There is a paramount need to develop new techniques and tools that will extract as much information as possible from the ever growing repository of protein 3D structures. We report here on the development of a software tool for the multiple superimposition of large sets of protein structural motifs. Our superimposition methodology performs a systematic search for the atom pairing that provides the best fit. During this search, the RMSD values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using PDB annotations for atoms. This approach guarantees that the best fit will be found and can be applied even when sequence similarity is low or does not exist at all. We have implemented this methodology in the Web application SiteBinder, which is able to process up to thousands of protein structural motifs in a very short time, and which provides an intuitive and user-friendly interface. Our benchmarking analysis has shown the robustness, efficiency, and versatility of our methodology and its implementation by the successful superimposition of 1000 experimentally determined structures for each of 32 eukaryotic linear motifs. We also demonstrate the applicability of SiteBinder using three case studies. We first compared the structures of 61 PA-IIL sugar binding sites containing nine different sugars, and we found that the sugar binding sites of PA-IIL and its mutants have a conserved structure despite their binding different sugars. We then superimposed over 300 zinc finger central motifs and revealed that the molecular structure in the vicinity of the Zn atom is highly conserved. Finally, we superimposed 12 BH3 domains from pro-apoptotic proteins. Our findings come to support the hypothesis that there is a structural basis for the functional segregation of BH3-only proteins into activators and enablers.

  18. Comparative genomics evidence that only protein toxins are tagging bad bugs

    Directory of Open Access Journals (Sweden)

    Kalliopi eGeorgiades

    2011-10-01

    Full Text Available The term toxin was introduced by Roux and Yersin and describes macromolecular substances that, when produced during infection or when introduced parenterally or orally, cause an impairment of physiological functions that lead to disease or to the death of the infected organism. Long after the discovery of toxins, early genetic studies on bacterial virulence demonstrated that removing a certain number of genes from pathogenic bacteria decreases their capacity to infect hosts. Each of the removed factors was therefore referred to as a virulence factor, and it was speculated that non-pathogenic bacteria lack such supplementary factors. However, many recent comparative studies demonstrate that the specialization of bacteria to eukaryotic hosts is associated with massive gene loss. We recently demonstrated that the only features that seem to characterize 12 epidemic bacteria are toxin-antitoxin (TA modules, which are addiction molecules in host bacteria. In this study, we investigated if protein toxins are indeed the only molecules specific to pathogenic bacteria by comparing 14 epidemic bacterial killers (bad bugs with their 14 closest non-epidemic relatives (controls. We found protein toxins in significantly more elevated numbers in all of the bad bugs. For the first time, statistical principal components analysis, including genome size, GC%, TA modules, restriction enzymes and toxins, revealed that toxins are the only proteins other than TA modules that are correlated with the pathogenic character of bacteria. Moreover, intracellular toxins appear to be more correlated with the pathogenic character of bacteria than secreted toxins. In conclusion, we hypothesize that the only truly identifiable phenomena, witnessing the convergent evolution of the most pathogenic bacteria for humans are the loss of metabolic activities, i.e., the outcome of the loss of regulatory and transcription factors and the presence of protein toxins, alone or coupled as TA

  19. Pregnancy-associated plasma protein-A deficiency improves survival of mice on a high fat diet.

    Science.gov (United States)

    Conover, Cheryl A; Bale, Laurie K; Marler, Ronald J

    2015-10-01

    Obesity is on the rise in westernized countries, and visceral obesity in particular is associated with enhanced risk of developing metabolic disease and accelerated aging. Various dietary restriction regimens have been shown to extend healthy lifespan in a variety of species. However, identification of alternative approaches that could be more acceptable to humans is actively being pursued. We have shown previously that mice deficient in pregnancy-associated plasma protein-A (PAPP-A) have an extended healthy lifespan on a regular chow diet. In this study, we determined the lifespan of PAPP-A knock-out (KO) and wild-type (WT) littermates fed a high fat diet (HFD) starting at 12 months of age. PAPP-A KO and WT mice had equivalent weight gain as measured over 25 weeks on HFD. However, PAPP-A KO mice on HFD had a significant increase in lifespan (P=0.018). Body composition and tissue pathology were assessed in a separate cohort of mice after 30 weeks on HFD. Percent body fat was equivalent in the two groups. However, there was a decrease in visceral fat depot weights and an increase in serum adiponectin levels in PAPP-A KO compared to WT mice. Major pathological differences were seen in kidney, heart and testes, with PAPP-A KO mice having little, if any, evidence of inflammation, mineralization, or degeneration in these tissues compared to WT mice. Thus, PAPP-A is a novel drug target with the potential to promote healthy longevity without a need for dietary restriction. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Comparable survival outcome of metastatic colorectal cancer in Indigenous and non-Indigenous patients: Retrospective analysis of the South Australian metastatic colorectal cancer registry.

    Science.gov (United States)

    Tomita, Yoko; Karapetis, Christos S; Roder, David; Beeke, Carol; Hocking, Christopher; Roy, Amitesh C; Townsend, Amanda R; Padbury, Rob; Maddern, Guy; Price, Timothy J

    2016-04-01

    This study aims to investigate disparities in demographics, disease characteristics, treatment and overall survival between South Australian (SA) Indigenous and non-Indigenous patients with metastatic colorectal cancer (mCRC). This employs a retrospective population study using the SA mCRC registry. The SA mCRC registry identifies mCRC patients from hospital encounters, histopathology reports, medical oncology letters, clinician notification, attendances at multidisciplinary meetings and death audits by the SA Cancer Registry. A total of 2865 adult mCRC patients including 14 Indigenous patients were identified through the SA mCRC registry between February 2006 and August 2013. Patients were linked to the SA Cancer Registry to obtain Indigenous status. Demographic, disease and treatment characteristics were compared using Chi-squared test and t-test; while overall survival defined as time to any cause of death was analysed using Cox regression. No difference was observed for clinical characteristics, except for a higher proportion of Indigenous patients receiving chemotherapy (85.7% versus 58.5%; P = 0.04). The rate of liver surgery was similar across the two groups (21.0% versus 15.1%; P = 0.40). The median overall survivals were equivalent (11.9 months versus 15.1 months; hazard ratio = 1.00; 95% confidence interval for hazard ratio, 0.54-1.86). Clinical characteristics and survival outcomes were similar between Indigenous and non-Indigenous patients captured on the SA mCRC registry, and outcome of those who have an access to comprehensive cancer care appeared independent of Indigenous status and in line with large clinical trials. Underestimation of Indigenous cases due to their lower utilisation of cancer service could not be excluded and ultimately the accurate reporting of these patients is crucial. © 2015 National Rural Health Alliance Inc.

  1. Health check-ups and family screening allow detection of hereditary hemochromatosis with less advanced liver fibrosis and survival comparable with the general population.

    Science.gov (United States)

    Aleman, Soo; Endalib, Sanam; Stål, Per; Lööf, Lars; Lindgren, Stefan; Sandberg-Gertzén, Hanna; Almer, Sven; Olsson, Sigvard; Danielsson, Ake; Wallerstedt, Sven; Hultcrantz, Rolf

    2011-09-01

    The information concerning the morbidity and mortality of hereditary hemochromatosis is based primarily on clinical cohorts of symptomatic patients. The major aim of this study was to analyze the long-term prognosis for Swedish patients with this condition, with respect to both clinical features and survival, in relation to the route by which the disease was detected. 373 patients with hemochromatosis detected through routine health check-ups (n = 153), family screening (n = 44), symptoms of arthralgia (n = 23), investigation of other diseases/symptoms (n = 108) or signs of liver disease (n = 45) were monitored for a mean period of 11.9 ± 5.8 years. The degree of liver fibrosis and survival were analyzed. Overall survival among these patients was not significantly different from that of a matched normal population. The patients diagnosed through health check-ups and family screening were detected at an earlier age and had the highest rate of survival. Liver biopsy at the time of diagnosis revealed cirrhosis in 9% of those detected through the health check-ups and 5% in the case of family screening, compared with 13% for the group with arthralgia, 17% for other diseases/symptoms and 42% for liver disease. Health check-ups and family screening allow detection of hereditary hemochromatosis at an earlier age and with less advanced liver fibrosis, although a few of these patients have already developed cirrhosis. Our study indicates that iron indices should be included in health check-ups, and if abnormal, should lead to further investigation.

  2. The Influence of Gastric Cancer Screening on the Stage at Diagnosis and Survival: A Meta-Analysis of Comparative Studies in the Far East.

    Science.gov (United States)

    Khanderia, Esha; Markar, Sheraz R; Acharya, Amish; Kim, Yeol; Kim, Young-Woo; Hanna, George B

    2016-03-01

    Gastric cancer is the fifth most common cancer and the second most common cause of cancer-related death worldwide. The aim of this review was to evaluate the effect of gastric cancer screening on the stage at diagnosis and survival from disease. A systematic review of the literature between January 1995 and December 2014 was performed. Studies that compared screened versus nonscreened populations for the diagnosis of gastric cancer and included the stage at diagnosis were analyzed. The QUADAS-2 and the ROBANS tools were used to assess the quality of the studies. A total of 11 studies from the Far East comprising 4039 participants in the screened and 6635 in the nonscreened groups were included. Screening was associated with a significant increase in the detection of early gastric cancer (EGC) [pooled odds ratio (POR)=3.90; 95% confidence interval (CI), 3.01-5.06; Pgastric cancer (POR=0.27; 95% CI, 0.20-0.35; Pscreening improved the 5-year survival significantly (hazard ratio=0.56; 95% CI, 0.48-0.66; Pscreened patients were found to have EGC compared with 43% of the nonscreened patients. About 8% of the screened patients were found to have advanced gastric cancer compared with 54% of the nonscreened patients. Screening for gastric cancer is useful in detecting asymptomatic patients with EGC in high-prevalence areas. This in turn increases the number of treatable cancers and improves the 5-year survival. There is a need for the development and the validation of alternative risk-stratification tools in low-incidence areas to allow for similar benefits.

  3. The NHE1 Na+/H+ exchanger recruits ezrin/radixin/moesin proteins to regulate Akt-dependent cell survival.

    Science.gov (United States)

    Wu, Karen L; Khan, Shenaz; Lakhe-Reddy, Sujata; Jarad, George; Mukherjee, Amitava; Obejero-Paz, Carlos A; Konieczkowski, Martha; Sedor, John R; Schelling, Jeffrey R

    2004-06-18

    Apoptosis results in cell shrinkage and intracellular acidification, processes opposed by the ubiquitously expressed NHE1 Na(+)/H(+) exchanger. In addition to mediating Na(+)/H(+) transport, NHE1 interacts with ezrin/radixin/moesin (ERM), which tethers NHE1 to cortical actin cytoskeleton to regulate cell shape, adhesion, motility, and resistance to apoptosis. We hypothesize that apoptotic stress activates NHE1-dependent Na(+)/H(+) exchange, and NHE1-ERM interaction is required for cell survival signaling. Apoptotic stimuli induced NHE1-regulated Na(+)/H(+) transport, as demonstrated by ethyl-N-isopropyl-amiloride-inhibitable, intracellular alkalinization. Ectopic NHE1, but not NHE3, expression rescued NHE1-null cells from apoptosis induced by staurosporine or N-ethylmaleimide-stimulated KCl efflux. When cells were subjected to apoptotic stress, NHE1 and phosphorylated ERM physically associated within the cytoskeleton-enriched fraction, resulting in activation of the pro-survival kinase, Akt. NHE1-associated Akt activity and cell survival were inhibited in cells expressing ERM binding-deficient NHE1, dominant negative ezrin constructs, or ezrin mutants with defective binding to phosphoinositide 3-kinase, an upstream regulator of Akt. We conclude that NHE1 promotes cell survival by dual mechanisms: by defending cell volume and pH(i) through Na(+)/H(+) exchange and by functioning as a scaffold for recruitment of a signalplex that includes ERM, phosphoinositide 3-kinase, and Akt.

  4. Posttraumatic stress disorder (PTSD) in children after paediatric intensive care treatment compared to children who survived a major fire disaster

    NARCIS (Netherlands)

    Bronner, M.B.; Knoester, H.; Bos, AP; Last, B.F.; Grootenhuis, M.A.

    2008-01-01

    Background: The goals were to determine the presence of posttraumatic stress disorder (PTSD) in children after paediatric intensive care treatment, to identify risk factors for PTSD, and to compare this data with data from a major fire disaster in the Netherlands. Methods: Children completed the

  5. Spectrophotometric determination of total proteins in blood plasma: a comparative study among dye-binding methods

    Directory of Open Access Journals (Sweden)

    Dimas Augusto Morozin Zaia

    2005-05-01

    Full Text Available A comparative study between the biuret method (standard method for total proteins and spectrophotometric methods using dyes (Bradford, 3',3",5',5"-tetrabromophenolphthalein ethyl ester-TBPEE, and erythrosin-B was carried out for the determination of total proteins in blood plasma from rats. Bradford method showed the highest sensitivity for proteins and biuret method showed the lowest. For all the methods, the absorbance for different proteins (BSA, casein, and egg albumin was measured and Bradford method showed the lowest variation of absorbance. The concentration of total protein obtained by using Bradford method was not statistically different (p>0.05 from concentration of total protein obtained by the biuret method. But in regard to erythrosin-B and TBPEE methods the concentrations of total protein were statistically different (pA determinação de proteínas totais em plasma sangüíneo é importante em diversas áreas de pesquisa. Um estudo comparativo entre o método de biureto (método padrão para proteínas totais e diversos métodos que utilizam corantes (Bradford, tetrabromofenolftaleína etil éster-TBPEE, e eritrosina-B foi realizado para a determinação de proteínas totais em plasma sangüíneo de ratos. O método de Bradford mostrou a maior sensibilidade para proteínas e o de biureto a menor. Para todos os métodos, as absorbâncias para diferentes proteínas (BSA, caseína, e ovoalbumina foram medidas e o método de Bradford mostrou a menor variação da absorbância. Utilizando o método de Bradford a concentração de proteínas totais obtida não foi estatisticamente diferente (p>0.05 daquela obtida pelo método do biureto. Porém, para os métodos da eritrosina-B e TBPEE as concentrações de proteínas totais foram estatisticamente diferentes (p<0.05 da obtida pelo método de biureto. Portanto o método de Bradford pode ser utilizado no lugar do método de biureto para a determinação de proteínas totais em plasma sangüíneo.

  6. Comparative study analyzing survival and safety of bevacizumab/carboplatin/paclitaxel versus carboplatin/docetaxel in initial treatment of metastatic Her-2-negative breast cancer

    Directory of Open Access Journals (Sweden)

    Abdel Kader Y

    2013-06-01

    Full Text Available Yasser Abdel Kader,1 Marc Spielmann,2 Tamer El-Nahas,1 Amr Sakr,1 Hassan Metwally31Department of Clinical Oncology, Cairo University, Cairo, Egypt; 2Department of Medical Oncology, Institute Gustave Rousssy, VuilleJuif, Paris, France; 3Department of Clinical Oncology, Monufia University, Monufia, EgyptPurpose: In view of the previous reports demonstrating the positive outcome of bevacizumab in metastatic breast cancer, we aimed at comparing the role of bevacizumab-based metronomic combination with taxane (paclitaxel versus a different taxane (docetaxel-based regimen in addition to carboplatin as initial treatment for metastatic Her-2-negative breast cancer.Patients and methods: This is a randomized Phase III study comparing the progression-free survival (PFS and safety in Her-2-negative female patients with initial diagnosis of metastatic breast cancer with World Health Organization performance status of 0–II. Forty-one patients were randomized from September 2008 to July 2009 to receive either; (1 bevacizumab 5 mg/kg day 1 and day 15, carboplatin area under the curve (AUC-2 day 1, day 8, and day 15, and paclitaxel 60 mg/m2 day 1, day 8, and day 15 (arm-I; or (2 carboplatin AUC-5 day 1, docetaxel 75 mg/m2 day 1 (arm-II. The Kaplan–Meier method was used for estimating survival; log-rank test for comparing survival curves. The primary end point was PFS, and secondary end points were overall survival (OS and safety.Results: PFS was 10 months in arm I versus 10.2 months in arm II (P = 0.9. The OS rate was similar in both arms: 37.6 months for arm I versus 37.4 months for arm II (P = 0.92. The toxicity revealed higher incidence of hypertension and proteinuria in arm I; however, with higher incidence of grade III–IV neutropenia and neutropenic fever in arm II. No treatment-related mortality was recorded.Conclusion: Bevacizumab/carboplatin/paclitaxel and carboplatin/docetaxel show comparable PFS and OS with different toxicity profiles

  7. Survival and cause of death after transcatheter aortic valve replacement as compared to an age- and sex-matched background population

    DEFF Research Database (Denmark)

    Theut, Marie; Thygesen, Julie B; De Backer, Ole

    2017-01-01

    AIMS: This study aimed to assess survival and causes of death in a real-world TAVR population as compared to an age- and sex-matched background population. METHODS AND RESULTS: Each aortic stenosis (AS) patient treated with TAVR in Eastern Denmark between 2007 and 2014 (n=617) was matched with 25...... age- and sex-matched controls (n=15,425) randomly drawn from the general Danish population. In the total TAVR population, early mortality (≤90 days) was significantly higher (hazard ratio [HR] 3.90 [2.82-5.39]; p

  8. Interactions of the integrin subunit beta1A with protein kinase B/Akt, p130Cas and paxillin contribute to regulation of radiation survival

    DEFF Research Database (Denmark)

    Seidler, Julia; Durzok, Rita; Brakebusch, Cord

    2005-01-01

    in presence or absence of growth factors or inhibitors for phosphatidylinositol-3 kinase (PI3K), i.e. Ly294002 and wortmannin. In addition to colony formation, protein kinase B/Akt (PKB/Akt) kinase activity, focal adhesion kinase (FAK), p130Cas, paxillin and c-Jun N2-terminal kinase (JNK) expression...... substrates. PI3K inhibition moderately or strongly radiosensitized GD25beta1A or GD25beta1B cells, respectively. The pro-survival effects detected in serum starved GD25beta1A cells were due to direct, PI3K-mediated stimulation of PKB/Akt activity by beta1-integrins and induced p130Cas and paxillin...... phosphorylation. Phosphorylated p130Cas and paxillin subsequently prevented activation of cell death-regulating JNK. CONCLUSIONS: The data show that beta1-integrin-mediated signaling through the cytoplasmic integrin domains is critical for efficient pro-survival regulation after irradiation. Profound knowledge...

  9. Comparative Survival Study (CSS) of Hatchery PIT-tagged Spring/Summer Chinook; Migration Years 1997-2000 Mark/Recapture Activities and Bootstrap Analysis, 2002 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Berggren Thomas J.; Franzoni, Henry; Basham, Larry R. (Columbia Basin Fish and Wildlife Authority, Fish Passage Center, Portland, OR)

    2005-04-01

    The Comparative Survival Study (CSS) was initiated in 1996 as a multi-year program of the fishery agencies and tribes to estimate survival rates over different life stages for spring and summer chinook (hereafter, chinook) produced in major hatcheries in the Snake River basin and from selected hatcheries in the lower Columbia River. Much of the information evaluated in the CSS is derived from fish tagged with Passive Integrated Transponder (PIT) tags. A comparison of survival rates of chinook marked in two different regions (which differ in the number of dams chinook have to migrate through) provides insight into the effects of the Snake/Columbia hydroelectric system (hydrosystem). The CSS also compares the smolt-to-adult survival rates (SARs) for Snake River chinook that were transported versus those that migrated in-river to below Bonneville Dam. Additional comparisons can be made within in-river experiences as well comparison between the different collector projects from which smolts are transported. CSS also compares these survival rates for wild Snake River spring and summer chinook. These comparisons generate information regarding the relative effects of the current management actions used to recover this listed species. Scientists and managers have recently emphasized the importance of delayed hydrosystem mortality to long-term management decisions. Delayed hydrosystem mortality may be related to the smolts experience in the Federal Columbia River Power System, and could occur for both smolts that migrate in-river and smolts that are transported. The CSS PIT tag information on in-river survival rates and smolt-to-adult survival rates (SARs) of transported and in-river fish are relevant to estimation of ''D'', which partially describes delayed hydrosystem mortality. The parameter D is the differential survival rate of transported fish relative to fish that migrate in-river, as measured from below Bonneville Dam to adults returning to Lower

  10. Excess mortality in men compared with women following a hip fracture. National analysis of comedications, comorbidity and survival

    DEFF Research Database (Denmark)

    Kannegaard, Pia Nimann; van der Mark, Susanne; Eiken, Pia

    2010-01-01

    INTRODUCTION: osteoporosis is a common disease, and the incidence of osteoporotic fractures is expected to rise with the growing elderly population. Immediately following, and probably several years after a hip fracture, patients, both men and women, have a higher risk of dying compared...... to the general population regardless of age. The aim of this study was to assess excess mortality following hip fracture and, if possible, identify reasons for the difference between mortality for the two genders. METHODS: this is a nationwide register-based cohort study presenting data from the National...... compared to the general population was 37.1% (9.9%) in men and 26.4% (9.3%) in women. In the first year, the risk of death significantly increased for women with increasing age (hazard ratio, HR: 1.06, 95% confidence interval, CI: 1.06-1.07), the number of comedications (HR 1.04, 95% CI 1...

  11. Comparative Costs and Conservation Policies for the Survival of the Oranutan and Other Species: Includes an Example

    OpenAIRE

    Tisdell, Clement A.; Swarna Nantha, Hemanath

    2010-01-01

    The extent to which conservation is feasible is constrained by budgets and the financial sacrifice stakeholders are willing to bear. Therefore a possible objective for conserving a species is to minimise the cost of achieving that stated aim. For example, if a minimum viable population (MVP) of a species is to be conserved, the size and type of habitats reserved for this could be selected to minimise cost. This requires consideration of the comparative (relative) opportunity costs of reservin...

  12. Excess mortality in men compared with women following a hip fracture. National analysis of comedications, comorbidity and survival

    DEFF Research Database (Denmark)

    Kannegaard, Pia Nimann; van der Mark, Susanne; Eiken, Pia Agnete

    2010-01-01

    osteoporosis is a common disease, and the incidence of osteoporotic fractures is expected to rise with the growing elderly population. Immediately following, and probably several years after a hip fracture, patients, both men and women, have a higher risk of dying compared to the general population...... regardless of age. The aim of this study was to assess excess mortality following hip fracture and, if possible, identify reasons for the difference between mortality for the two genders....

  13. Inhibition of protein synthesis on the ribosome by tildipirosin compared with other veterinary macrolides.

    Science.gov (United States)

    Andersen, Niels Møller; Poehlsgaard, Jacob; Warrass, Ralf; Douthwaite, Stephen

    2012-11-01

    Tildipirosin is a 16-membered-ring macrolide developed to treat bacterial pathogens, including Mannheimia haemolytica and Pasteurella multocida, that cause respiratory tract infections in cattle and swine. Here we evaluated the efficacy of tildipirosin at inhibiting protein synthesis on the ribosome (50% inhibitory concentration [IC(50)], 0.23 ± 0.01 μM) and compared it with the established veterinary macrolides tylosin, tilmicosin, and tulathromycin. Mutation and methylation at key rRNA nucleotides revealed differences in the interactions of these macrolides within their common ribosomal binding site.

  14. Comparative Analysis of Protein Glycosylation Pathways in Humans and the Fungal Pathogen Candida albicans

    Directory of Open Access Journals (Sweden)

    Iván Martínez-Duncker

    2014-01-01

    Full Text Available Protein glycosylation pathways are present in all kingdoms of life and are metabolic pathways found in all the life kingdoms. Despite sharing commonalities in their synthesis, glycans attached to glycoproteins have species-specific structures generated by the presence of different sets of enzymes and acceptor substrates in each organism. In this review, we present a comparative analysis of the main glycosylation pathways shared by humans and the fungal pathogen Candida albicans: N-linked glycosylation, O-linked mannosylation and glycosylphosphatidylinositol-anchorage. The knowledge of similarities and divergences between these metabolic pathways could help find new pharmacological targets for C. albicans infection.

  15. Lesser suppression of energy intake by orally ingested whey protein in healthy older men compared with young controls.

    Science.gov (United States)

    Giezenaar, Caroline; Trahair, Laurence G; Rigda, Rachael; Hutchison, Amy T; Feinle-Bisset, Christine; Luscombe-Marsh, Natalie D; Hausken, Trygve; Jones, Karen L; Horowitz, Michael; Chapman, Ian; Soenen, Stijn

    2015-10-15

    Protein-rich supplements are used widely for the management of malnutrition in young and older people. Protein is the most satiating of the macronutrients in young. It is not known how the effects of oral protein ingestion on energy intake, appetite, and gastric emptying are modified by age. The aim of the study was to determine the suppression of energy intake by protein compared with control and underlying gastric-emptying and appetite responses of oral whey protein drinks in eight healthy older men (69-80 yr) compared with eight young male controls (18-34 yr). Subjects were studied on three occasions to determine the effects of protein loads of 30 g/120 kcal and 70 g/280 kcal compared with a flavored water control-drink (0 g whey protein) on energy intake (ad libitum buffet-style meal), and gastric emptying (three-dimensional-ultrasonography) and appetite (0-180 min) in a randomized, double-blind, cross-over design. Energy intake was suppressed by the protein compared with control (P = 0.034). Suppression of energy intake by protein was less in older men (1 ± 5%) than in young controls (15 ± 2%; P = 0.008). Cumulative energy intake (meal+drink) on the protein drink days compared with the control day increased more in older (18 ± 6%) men than young (1 ± 3%) controls (P = 0.008). Gastric emptying of all three drinks was slower in older men (50% gastric-emptying time: 68 ± 5 min) than young controls (36 ± 5 min; P = 0.007). Appetite decreased in young, while it increased in older (P protein-induced suppression of energy intake by whey protein compared with young controls, so that in the elderly men, protein ingestion increased overall energy intake more than in the young men. Copyright © 2015 the American Physiological Society.

  16. Vegetarian compared with meat dietary protein source and phosphorus homeostasis in chronic kidney disease.

    Science.gov (United States)

    Moe, Sharon M; Zidehsarai, Miriam P; Chambers, Mary A; Jackman, Lisa A; Radcliffe, J Scott; Trevino, Laurie L; Donahue, Susan E; Asplin, John R

    2011-02-01

    Patients with advanced chronic kidney disease (CKD) are in positive phosphorus balance, but phosphorus levels are maintained in the normal range through phosphaturia induced by increases in fibroblast growth factor-23 (FGF23) and parathyroid hormone (PTH). This provides the rationale for recommendations to restrict dietary phosphate intake to 800 mg/d. However, the protein source of the phosphate may also be important. We conducted a crossover trial in nine patients with a mean estimated GFR of 32 ml/min to directly compare vegetarian and meat diets with equivalent nutrients prepared by clinical research staff. During the last 24 hours of each 7-day diet period, subjects were hospitalized in a research center and urine and blood were frequently monitored. The results indicated that 1 week of a vegetarian diet led to lower serum phosphorus levels and decreased FGF23 levels. The inpatient stay demonstrated similar diurnal variation for blood phosphorus, calcium, PTH, and urine fractional excretion of phosphorus but significant differences between the vegetarian and meat diets. Finally, the 24-hour fractional excretion of phosphorus was highly correlated to a 2-hour fasting urine collection for the vegetarian diet but not the meat diet. In summary, this study demonstrates that the source of protein has a significant effect on phosphorus homeostasis in patients with CKD. Therefore, dietary counseling of patients with CKD must include information on not only the amount of phosphate but also the source of protein from which the phosphate derives.

  17. Species, biotype, and bacteriophage type determinations compared with cell envelope protein profiles for typing Acinetobacter strains.

    Science.gov (United States)

    Bouvet, P J; Jeanjean, S; Vieu, J F; Dijkshoorn, L

    1990-02-01

    Species, biotypes, and phage types were determined for 120 Acinetobacter strains from clinical or environmental sources or from culture collections. These characteristics were compared with cell envelope protein profiles obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in previous studies. A considerable heterogeneity of species and types was observed by use of the various methods, in particular among strains from different sources. Acinetobacter baumannii was the most commonly found species in isolates from clinical sources, followed by Acinetobacter species 3. Nine biotypes were observed among A. baumannii strains. Further differentiation within most species and biotypes was achieved by protein profile typing and, to some extent, phage typing. Of 120 strains, 49 (41%) were not typeable by phages. Consistent results for the various classification methods were obtained for strains from common sources. Biotyping seemed an appropriate method for the screening of strains, whereas protein profile and phage typing could serve as additional methods to establish the identity or nonidentity of strains. Results of this study suggest that the combination of the typing methods is useful in epidemiological studies.

  18. Comparative evaluation of heterologous production systems for recombinant pulmonary surfactant protein D

    Directory of Open Access Journals (Sweden)

    Daniela eSalgado

    2014-12-01

    Full Text Available Commercial surfactant products derived from animal lungs are used for the treatment of respiratory diseases in premature neonates. These products contain lipids and the hydrophobic surfactant proteins B and C, which help to lower the surface tension in the lungs. Surfactant products are less effective when pulmonary diseases involve inflammatory complications because two hydrophilic surfactant proteins (A and D are lost during the extraction process, yet surfactant protein D (SP-D is a component of the innate immune system that helps to reduce lung inflammation. The performance of surfactant products could therefore be improved by supplementing them with an additional source of SP-D. Recombinant SP-D is produced in mammalian cells and bacteria (Escherichia coli, and also experimentally in the yeast Pichia pastoris. Mammalian cells produce full-size SP-D, but the yields are low and the cost of production is high. In contrast, bacteria produce a truncated form of SP-D, which is active in vitro and in vivo, and higher yields can be achieved at a lower cost. We compare the efficiency of production of recombinant SP-D in terms of the total yields achieved in each system and the amount of SP-D needed to meet the global demand for the treatment of pulmonary diseases, using respiratory distress syndrome as a case study.

  19. Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P

    Directory of Open Access Journals (Sweden)

    Manoj P. Samanta

    2016-04-01

    Full Text Available RNase P, a ribozyme-based ribonucleoprotein (RNP complex that catalyzes tRNA 5′-maturation, is ubiquitous in all domains of life, but the evolution of its protein components (RNase P proteins, RPPs is not well understood. Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and eukaryotic (homologous RPPs, which are unrelated to the single bacterial RPP. Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome complexes, which may indicate coevolution/coordinate regulation of RNase P with other core cellular machineries. Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the relative frequency of residues at every position in the context of the high-resolution structures of each of the RPPs (either alone or as functional binary complexes, we suggest residues for mutational analysis that may help uncover structure-function relationships in RPPs.

  20. Brachytherapy Improves Biochemical Failure–Free Survival in Low- and Intermediate-Risk Prostate Cancer Compared With Conventionally Fractionated External Beam Radiation Therapy: A Propensity Score Matched Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Graham D. [University of Western Ontario, London, Ontario (Canada); Pickles, Tom [Department of Radiation Oncology, British Columbia Cancer Agency, Vancouver, British Columbia (Canada); Crook, Juanita [Department of Radiation Oncology, Kelowna General Hospital, Kelowna, British Columbia (Canada); Martin, Andre-Guy; Vigneault, Eric [Department of Radiation Oncology, L' Hotel Dieu de Quebec, Quebec City, Quebec (Canada); Cury, Fabio L. [Department of Radiation Oncology, Montreal General Hospital, Montreal, Quebec (Canada); Morris, Jim [Department of Radiation Oncology, British Columbia Cancer Agency, Vancouver, British Columbia (Canada); Catton, Charles [Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, Ontario (Canada); Lukka, Himu [Department of Radiation Oncology, Juravinski Cancer Centre, Hamilton, Ontario (Canada); Warner, Andrew [Department of Radiation Oncology, London Health Sciences Center, London, Ontario (Canada); Yang, Ying [University of Waterloo, Waterloo, Ontario (Canada); Rodrigues, George, E-mail: George.Rodrigues@lhsc.on.ca [University of Western Ontario, London, Ontario (Canada); Department of Radiation Oncology, London Health Sciences Center, London, Ontario (Canada)

    2015-03-01

    Purpose: To compare, in a retrospective study, biochemical failure-free survival (bFFS) and overall survival (OS) in low-risk and intermediate-risk prostate cancer patients who received brachytherapy (BT) (either low-dose-rate brachytherapy [LDR-BT] or high-dose-rate brachytherapy with external beam radiation therapy [HDR-BT+EBRT]) versus external beam radiation therapy (EBRT) alone. Methods and Materials: Patient data were obtained from the ProCaRS database, which contains 7974 prostate cancer patients treated with primary radiation therapy at four Canadian cancer institutions from 1994 to 2010. Propensity score matching was used to obtain the following 3 matched cohorts with balanced baseline prognostic factors: (1) low-risk LDR-BT versus EBRT; (2) intermediate-risk LDR-BT versus EBRT; and (3) intermediate-risk HDR-BT+EBRT versus EBRT. Kaplan-Meier survival analysis was performed to compare differences in bFFS (primary endpoint) and OS in the 3 matched groups. Results: Propensity score matching created acceptable balance in the baseline prognostic factors in all matches. Final matches included 2 1:1 matches in the intermediate-risk cohorts, LDR-BT versus EBRT (total n=254) and HDR-BT+EBRT versus EBRT (total n=388), and one 4:1 match in the low-risk cohort (LDR-BT:EBRT, total n=400). Median follow-up ranged from 2.7 to 7.3 years for the 3 matched cohorts. Kaplan-Meier survival analysis showed that all BT treatment options were associated with statistically significant improvements in bFFS when compared with EBRT in all cohorts (intermediate-risk EBRT vs LDR-BT hazard ratio [HR] 4.58, P=.001; intermediate-risk EBRT vs HDR-BT+EBRT HR 2.08, P=.007; low-risk EBRT vs LDR-BT HR 2.90, P=.004). No significant difference in OS was found in all comparisons (intermediate-risk EBRT vs LDR-BT HR 1.27, P=.687; intermediate-risk EBRT vs HDR-BT+EBRT HR 1.55, P=.470; low-risk LDR-BT vs EBRT HR 1.41, P=.500). Conclusions: Propensity score matched analysis showed that BT options led

  1. Posttraumatic stress disorder (PTSD in children after paediatric intensive care treatment compared to children who survived a major fire disaster

    Directory of Open Access Journals (Sweden)

    Last Bob F

    2008-05-01

    Full Text Available Abstract Background The goals were to determine the presence of posttraumatic stress disorder (PTSD in children after paediatric intensive care treatment, to identify risk factors for PTSD, and to compare this data with data from a major fire disaster in the Netherlands. Methods Children completed the Dutch Children's Responses to Trauma Inventory at three and nine months after discharge from the paediatric intensive care unit (PICU. Comparison data were available from 355 children survivors who completed the same questionnaire 10 months after a major fire disaster. Results Thirty-six children aged eight to 17 years completed questionnaires at three month follow-up, nine month follow-up, or both. More than one third (34.5% of the children had subclinical PTSD, while 13.8% were likely to meet criteria for PTSD. Maternal PTSD was the strongest predictor for child PTSD. There were no significant differences in (subclinical PTSD symptoms either over time or compared to symptoms of survivors from the fire disaster. Conclusion This study shows that a considerable number of children have persistent PTSD after PICU treatment. Prevention of PTSD is important to minimize the profound adverse effects that PTSD can have on children's well-being and future development.

  2. Posttraumatic stress disorder (PTSD) in children after paediatric intensive care treatment compared to children who survived a major fire disaster

    Science.gov (United States)

    Bronner, Madelon B; Knoester, Hendrika; Bos, Albert P; Last, Bob F; Grootenhuis, Martha A

    2008-01-01

    Background The goals were to determine the presence of posttraumatic stress disorder (PTSD) in children after paediatric intensive care treatment, to identify risk factors for PTSD, and to compare this data with data from a major fire disaster in the Netherlands. Methods Children completed the Dutch Children's Responses to Trauma Inventory at three and nine months after discharge from the paediatric intensive care unit (PICU). Comparison data were available from 355 children survivors who completed the same questionnaire 10 months after a major fire disaster. Results Thirty-six children aged eight to 17 years completed questionnaires at three month follow-up, nine month follow-up, or both. More than one third (34.5%) of the children had subclinical PTSD, while 13.8% were likely to meet criteria for PTSD. Maternal PTSD was the strongest predictor for child PTSD. There were no significant differences in (subclinical) PTSD symptoms either over time or compared to symptoms of survivors from the fire disaster. Conclusion This study shows that a considerable number of children have persistent PTSD after PICU treatment. Prevention of PTSD is important to minimize the profound adverse effects that PTSD can have on children's well-being and future development. PMID:18489798

  3. [Comparative study of two enteral feeding formulas in hospitalized elders: casein versus soybean protein].

    Science.gov (United States)

    García-Talavera Espín, N V; Gómez Sánchez, M B; Zomeño Ros, A I; Nicolás Hernández, M; González Valverde, F M; Gómez Ramos, M J; Sánchez Alvarez, C

    2010-01-01

    To compare the incidence of gastrointestinal side effects of two enteral feeding formulas with changes in the origin of protein (casein and isolated soy protein) in hospitalised elderly patients. A cross sectional survey was done among a sample of elderly patients carrying nasogastric tube admitted to the Reina Sofia General Hospital (Murcia) during a period of 6 months. A formula based on casein or soybean protein was randomly assigned. The variables studied were: age, sex, cause for indication of EN, duration of the EN and maximum amount of EN administered per day. Nutritional status at admission and discharge, mortality and gastrointestinal side effects (diarrhoea, constipation, vomits or regurgitation) were also collected. Statistical analyses were performed with the Student's T and chi 2 tests, with a significance of 95%. Sample conformed by 50 patients over 65 years (48% casein, 52% soybean) without statistically significant differences in age nor cause of indication of the EN. Either there were no differences in the nutritional status at the admission and discharge in both groups. Significant differences were observed in the incidence of diarrhoea (C: 45.83%, S: 7.69%, p = 0.009) and vomits (C: 41.66%, S: 15.38%, p = 0.05). A significant reduction in the incidence of gastrointestinal complications, a reduction in the incidence of ulcers by pressure and less mortality occurred on the group that took formula based on the soybean protein. The individualized nutritional evaluation must be performed routinely when the patient is admitted to the hospital for detection and treatment of early signs of malnutrition.

  4. Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors

    DEFF Research Database (Denmark)

    Nguyen, E.D.; Meiler, J.; Norn, C.

    2013-01-01

    The rapidly increasing number of high-resolution X-ray structures of G-protein coupled receptors (GPCRs) creates a unique opportunity to employ comparative modeling and docking to provide valuable insight into the function and ligand binding determinants of novel receptors, to assist in virtual...... and side-chain conformational space with Rosetta can be leveraged to meet this challenge. This study performs unbiased comparative modeling and docking methodologies using 14 distinct high-resolution GPCRs and proposes knowledge-based filtering methods for improvement of sampling performance...... and identification of correct ligand-receptor interactions. On average, top ranked receptor models built on template structures over 50% sequence identity are within 2.9 Å of the experimental structure, with an average root mean square deviation (RMSD) of 2.2 Å for the transmembrane region and 5 Å for the second...

  5. Expression of Proteins Involved in Epithelial-Mesenchymal Transition as Predictors of Metastasis and Survival in Breast Cancer Patients

    Science.gov (United States)

    2012-11-01

    critical prognostic factor for future recurrence and survival. Understanding the epidemiology and biology of metastasis could lead to better...Work. Training Plan, months 13-24 Tasks 1 and 5. All didactic predoctoral program requirements have been completed. Oral proposal defense was...metastases. Tumor size appears to affect lymph node metastasis differently by race, a mechanism that is modified by tumor biology . Our findings support the

  6. Surface-exposed proteins of pathogenic mycobacteria and the role of cu-zn superoxide dismutase in macrophages and neutrophil survival.

    Science.gov (United States)

    McNamara, Michael; Tzeng, Shin-Cheng; Maier, Claudia; Wu, Martin; Bermudez, Luiz E

    2013-11-28

    Pathogenic mycobacteria are important agents causing human disease. Mycobacterium avium subsp. hominissuis (M. avium) is a species of recalcitrant environmental pathogen. The bacterium forms robust biofilms that allow it to colonize and persist in austere environments, such as residential and commercial water systems. M. avium is also an opportunistic pathogen that is a significant source of mortality for immune-compromised individuals. Proteins exposed at the bacterial surface play a central role in mediating the relationship between the bacterium and its environment. The processes underlying both biofilm formation and pathogenesis are directly dependent on this essential subset of the bacterial proteome. Therefore, the characterization of the surface-exposed proteome is an important step towards an improved understanding of the mycobacterial biology and pathogenesis. Here we examined the complement of surface exposed proteins from Mycobacterium avium 104, a clinical isolate and reference strain of Mycobacterium avium subsp. hominissuis. To profile the surface-exposed proteins of viable M. avium 104, bacteria were covalently labeled with a membrane impermeable biotinylation reagent and labeled proteins were affinity purified via the biotin-streptavidin interaction. The results provide a helpful snapshot of the surface-exposed proteome of this frequently utilized reference strain of M. avium. A Cu-Zn SOD knockout mutant, MAV_2043, a surface identified protein, was evaluated regarding its role in the survival in both macrophages and neutrophils.

  7. A Systematic Review of the Effects of Plant Compared with Animal Protein Sources on Features of Metabolic Syndrome.

    Science.gov (United States)

    Chalvon-Demersay, Tristan; Azzout-Marniche, Dalila; Arfsten, Judith; Egli, Léonie; Gaudichon, Claire; Karagounis, Leonidas G; Tomé, Daniel

    2017-03-01

    Dietary protein may play an important role in the prevention of metabolic dysfunctions. However, the way in which the protein source affects these dysfunctions has not been clearly established. The aim of the current systematic review was to compare the impact of plant- and animal-sourced dietary proteins on several features of metabolic syndrome in humans. The PubMed database was searched for both chronic and acute interventional studies, as well as observational studies, in healthy humans or those with metabolic dysfunctions, in which the impact of animal and plant protein intake was compared while using the following variables: cholesterolemia and triglyceridemia, blood pressure, glucose homeostasis, and body composition. Based on data extraction, we observed that soy protein consumption (with isoflavones), but not soy protein alone (without isoflavones) or other plant proteins (pea and lupine proteins, wheat gluten), leads to a 3% greater decrease in both total and LDL cholesterol compared with animal-sourced protein ingestion, especially in individuals with high fasting cholesterol concentrations. This observation was made when animal proteins were provided as a whole diet rather than given supplementally. Some observational studies reported an inverse association between plant protein intake and systolic and diastolic blood pressure, but this was not confirmed by intervention studies. Moreover, plant protein (wheat gluten, soy protein) intake as part of a mixed meal resulted in a lower postprandial insulin response than did whey. This systematic review provides some evidence that the intake of soy protein associated with isoflavones may prevent the onset of risk factors associated with cardiovascular disease, i.e., hypercholesterolemia and hypertension, in humans. However, we were not able to draw any further conclusions from the present work on the positive effects of plant proteins relating to glucose homeostasis and body composition. © 2017 American

  8. The cost of surviving nitrogen excess: energy and protein demand in the lichen Cladonia portentosa as revealed by proteomic analysis.

    Science.gov (United States)

    Munzi, Silvana; Sheppard, Lucy J; Leith, Ian D; Cruz, Cristina; Branquinho, Cristina; Bini, Luca; Gagliardi, Assunta; Cai, Giampiero; Parrotta, Luigi

    2017-04-01

    Different nitrogen forms affect different metabolic pathways in lichens. In particular, the most relevant changes in protein expression were observed in the fungal partner, with NO 3- mostly affecting the energetic metabolism and NH 4+ affecting transport and regulation of proteins and the energetic metabolism much more than NO 3- did. Excess deposition of reactive nitrogen is a well-known agent of stress for lichens, but which symbiont is most affected and how, remains a mystery. Using proteomics can expand our understanding of stress effects on lichens. We investigated the effects of different doses and forms of reactive nitrogen, with and without supplementary phosphorus and potassium, on the proteome of the lichen Cladonia portentosa growing in a 'real-world' simulation of nitrogen deposition. Protein expression changed with the nitrogen treatments but mostly in the fungal partner, with NO3- mainly affecting the energetic metabolism and NH4+ also affecting the protein synthesis machinery. The photobiont mainly responded overexpressing proteins involved in energy production. This suggests that in response to nitrogen stress, the photobiont mainly supports the defensive mechanisms initiated by the mycobiont with an increased energy production. Such surplus energy is then used by the cell to maintain functionality in the presence of NO3-, while a futile cycle of protein production can be hypothesized to be induced by NH4+ excess. External supply of potassium and phosphorus influenced differently the responses of particular enzymes, likely reflecting the many processes in which potassium exerts a regulatory function.

  9. The Princeton Protein Orthology Database (P-POD: a comparative genomics analysis tool for biologists.

    Directory of Open Access Journals (Sweden)

    Sven Heinicke

    2007-08-01

    Full Text Available Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases combine results from multiple comparative genomics methods with manually curated information from the literature. Here we describe the Princeton Protein Orthology Database (P-POD, http://ortholog.princeton.edu, a user-friendly database system that allows users to find and visualize the phylogenetic relationships among predicted orthologs (based on the OrthoMCL method to a query gene from any of eight eukaryotic organisms, and to see the orthologs in a wider evolutionary context (based on the Jaccard clustering method. In addition to the phylogenetic information, the database contains experimental results manually collected from the literature that can be compared to the computational analyses, as well as links to relevant human disease and gene information via the OMIM, model organism, and sequence databases. Our aim is for the P-POD resource to be extremely useful to typical experimental biologists wanting to learn more about the evolutionary context of their favorite genes. P-POD is based on the commonly used Generic Model Organism Database (GMOD schema and can be downloaded in its entirety for installation on one's own system. Thus, bioinformaticians and software developers may also find P-POD useful because they can use the P-POD database infrastructure when developing their own comparative genomics resources and database tools.

  10. C4b binding protein binds to CD154 preventing CD40 mediated cholangiocyte apoptosis: a novel link between complement and epithelial cell survival.

    Directory of Open Access Journals (Sweden)

    Kevin T Williams

    Full Text Available Activation of CD40 on hepatocytes and cholangiocytes is critical for amplifying Fas-mediated apoptosis in the human liver. C4b-Binding Protein (C4BP has been reported to act as a potential surrogate ligand for CD40, suggesting that it could be involved in modulating liver epithelial cell survival. Using surface plasmon resonance (BiaCore analysis supported by gel filtration we have shown that C4BP does not bind CD40, but it forms stable high molecular weight complexes with soluble CD40 ligand (sCD154. These C4BP/sCD154 complexes bound efficiently to immobilised CD40, but when applied to cholangiocytes they failed to induce apoptosis or proliferation or to activate NFkB, AP-1 or STAT 3, which are activated by sCD154 alone. Thus C4BP can modulate CD40/sCD154 interactions by presenting a high molecular weight multimeric sCD154/C4BP complex that suppresses critical intracellular signalling pathways, permitting cell survival without inducing proliferation. Immunohistochemistry demonstrated co-localisation and enhanced expression of C4BP and CD40 in human liver cancers. These findings suggest a novel pathway whereby components of the complement system and TNF ligands and receptors might be involved in modulating epithelial cell survival in chronic inflammation and malignant disease.

  11. Early response of C-reactive protein as a predictor of survival in patients with metastatic renal cell carcinoma treated with tyrosine kinase inhibitors.

    Science.gov (United States)

    Yasuda, Yosuke; Saito, Kazutaka; Yuasa, Takeshi; Uehara, Sho; Kawamura, Naoko; Yokoyama, Minato; Ishioka, Junichiro; Matsuoka, Yoh; Yamamoto, Shinya; Okuno, Tetsuo; Yonese, Junji; Kihara, Kazunori; Fujii, Yasuhisa

    2017-12-01

    Pretreatment C-reactive protein (CRP) has been shown to be an independent prognostic factor for metastatic renal cell carcinoma (mRCC) treated with tyrosine kinase inhibitors (TKIs). We further evaluated the early response of CRP after the initiation of TKIs. A total of 103 patients (80 men and 23 women) were treated with TKIs for mRCC from 2008-2013. Patients were divided into three groups according to their early CRP kinetics-patients whose baseline CRP levels were 20% at 4 weeks after the initiation of TKIs (early CRP responder), and the remaining patients (non-early CRP responder). The endpoints were progression-free survival (PFS) and overall survival (OS). The median follow-up period was 21 (interquartile range 10-34) months. The numbers of patients classified as non-elevated, early CRP responder, and non-early CRP responder were 62, 19, and 22, respectively. The 1-year PFS rates of patients in the non-elevated, early CRP responder, and non-early CRP responder groups were 50, 23, and 9.7%, respectively (p < 0.001). The 1-year OS rates of patients in these three groups were 79, 62, and 36%, respectively (p < 0.001). In multivariate analysis, the early CRP kinetics assessment was a significant independent factor for PFS and OS. Early CRP response at 4 weeks is predictive of survival for patients with mRCC treated with TKI.

  12. Prediction of survival in resected non-small cell lung cancer using a protein expression-based risk model: implications for personalized chemoprevention and therapy.

    Science.gov (United States)

    Gold, Kathryn A; Kim, Edward S; Liu, Diane D; Yuan, Ping; Behrens, Carmen; Solis, Luisa M; Kadara, Humam; Rice, David C; Wistuba, Ignacio I; Swisher, Stephen G; Hofstetter, Wayne L; Lee, J Jack; Hong, Waun K

    2014-04-01

    Patients with resected non-small cell lung cancer (NSCLC) are at risk for recurrence of disease, but we do not have tools to predict which patients are at highest risk. We set out to create a risk model incorporating both clinical data and biomarkers. We assembled a comprehensive database with archival tissues and clinical follow-up from patients with NSCLC resected between 2002 and 2005. Twenty-one proteins identified from our preclinical studies as related to lung carcinogenesis were investigated, including pathways related to metabolism, DNA repair, inflammation, and growth factors. Expression of proteins was quantified using immunohistochemistry. Immunohistochemistry was chosen because it is widely available and can be performed on formalin-fixed paraffin-embedded specimens. Cox models were fitted to estimate effects of clinical factors and biomarkers on recurrence-free survival (RFS) and overall survival (OS). A total of 370 patients are included in our analysis. With median follow-up of 5.3 years, median OS is 6.4 years. A total of 209 cases with recurrence or death were observed. Multicovariate risk models for RFS and OS were developed including relevant biomarkers, age, and stage. Increased expression of phospho-adenosine monophosphate-activated protein kinase (pAMPK), phospho-mTOR (pmTOR), epithelial cell adhesion molecule (EpCAM), and calcium/calmodulin-dependent serine protein kinase were significant (P < 0.05) predictors for favorable RFS; insulin receptor, chemokine (C-X-C motif) receptor 2 (CXCR2), and insulin-like growth factor-1 receptor predicted for unfavorable RFS. Significant (P < 0.05) predictors for favorable OS include pAMPK, pmTOR, and EpCAM; CXCR2 and flap structure-specific endonuclease-1 predicted unfavorable OS. We have developed a comprehensive risk model predictive for recurrence in our large retrospective database, which is one of the largest reported series of resected NSCLC. ©2013 AACR.

  13. Characterization of virulence profile, protein secretion and immunogenicity of different Sporothrix schenckii sensu stricto isolates compared with S. globosa and S. brasiliensis species.

    Science.gov (United States)

    Fernandes, Geisa Ferreira; dos Santos, Priscila Oliveira; Rodrigues, Anderson Messias; Sasaki, Alexandre Augusto; Burger, Eva; de Camargo, Zoilo Pires

    2013-04-01

    A comparative study about protein secretion, immunogenicity and virulence was performed in order to characterize and to compare eight Sporothrix schenckii sensu stricto isolates. For virulence characterization, a murine model, based on survival assay and CFU counting was used. S. brasiliensis and S. globosa, a highly virulent and a non-virulent isolates, respectively were used as external controls. Exoantigen profiles showed different secreted molecules; the 46- and 60-kDa molecules were commonly secreted by all three species. The S. schenckii s. str. isolates could be classified as non-virulent or presenting low, medium or high virulence, based on survival times after infection and recovery of viable fungi. The humoral response profiles of mice infected with S. schenckii s. str., S. globosa and S. brasiliensis were heterogeneous; five virulent isolates (S. schenckii s. str., n = 4 and S. brasiliensis, n = 1) had in common the recognition of the 60-kDa molecule by their respective antisera, suggesting that this antigen may be involved in virulence. Furthermore, the 110-kDa molecule was secreted and recognized by antisera from four virulent isolates (S. schenckii s. str., n = 3 and S. brasiliensis, n = 1), so there is a possibility that this molecule is also related to virulence. Our findings reveal different degrees of virulence in S. schenckii s. str. isolates and suggest the correlation of protein secretion and immunogenicity with virulence of S. schenckii complex. These findings provide new insights into the pathogenesis of S. schenckii s. str. and improve the knowledge about immunogenicity and protein profiles in S. schenckii complex.

  14. Pregnancy-associated plasma protein-A predicts survival in end-stage renal disease-confounding and modifying effects of cardiovascular disease, body composition and inflammation.

    Science.gov (United States)

    Nilsson, Erik; Cao, Yang; Lindholm, Bengt; Ohyama, Ayane; Carrero, Juan Jesus; Qureshi, Abdul Rashid; Stenvinkel, Peter

    2017-07-24

    High pregnancy-associated plasma protein-A (PAPP-A) levels are linked to atherosclerosis and associate with increased mortality in prevalent dialysis patients. We investigated associations of PAPP-A, measured at dialysis initiation, with cardiovascular disease (CVD), CVD risk factors and mortality in incident dialysis patients, and explored if body composition and inflammation modulated these associations. Baseline plasma PAPP-A levels, inflammation biomarkers and body composition, using dual-energy X-ray absorptiometry, were measured in 286 incident dialysis patients. Primary outcome was survival during 60 months follow-up. Quantile (median) regression was used for cross-sectional analysis and Kaplan-Meier diagrams and Cox proportional hazards regression for survival analysis. In cross-sectional analysis adjusted for age and sex, PAPP-A levels were associated with lean tissue index (LTI) and high-sensitivity C-reactive protein (hsCRP) but not with fat tissue index (FTI) or history of CVD. In a model also including diabetes mellitus (DM), the association with LTI did not remain statistically significant. When adjusted for cardiovascular risk factors and body composition, higher PAPP-A levels showed a moderate but significant association [hazard ratio (HR) = 1.2, 95% confidence interval (CI): 1-1.4, P = 0.04] with mortality. When also including hsCRP the association was attenuated (HR = 1.2, 95% CI: 0.99-1.4, P = 0.06). In survival analysis, interactions with PAPP-A on the multiplicative scale were found for hsCRP (HR = 1.6, 95% CI: 1.2-2.2, P = 0.004) and DM (HR = 1.6, 95% CI: 1.1-2.2, P = 0.01) and with DM and FTI on the additive scale. Higher PAPP-A levels are associated with worse survival in incident dialysis patients following adjustment for established cardiovascular risk factors and body composition indices, but not clearly so when adjusted for hsCRP. Inflammation, body composition (FTI) and DM were found to be potential

  15. The Bacillus subtilis sigma(X) protein is an extracytoplasmic function sigma factor contributing to survival at high temperature.

    OpenAIRE

    Huang, X; Decatur, A; Sorokin, A.; Helmann, J D

    1997-01-01

    The sigX gene, identified as part of the international effort to sequence the Bacillus subtilis genome, has been proposed to encode an alternative sigma factor of the extracytoplasmic function (ECF) subfamily. The sigX gene is cotranscribed with a downstream gene, ypuN, during logarithmic and early stationary phases of growth. We now report that strains lacking sigma(X) are impaired in the ability to survive at high temperature whereas a ypuN mutant has increased thermotolerance. We overprodu...

  16. Effects of a supra-sustained gelatin-milk protein diet compared with (supra-)sustained milk protein diets on body-weight loss.

    Science.gov (United States)

    Hochstenbach-Waelen, Ananda; Soenen, Stijn; Westerterp, Klaas R; Westerterp-Plantenga, Margriet S

    2011-05-01

    Diets higher in protein content result in increased satiety and energy expenditure. In the short term, gelatin showed stronger hunger suppression and less subsequent energy intake compared with other proteins. The present study investigated whether a supra-sustained gelatin-milk protein (GMP) diet promotes weight loss compared with a sustained milk protein (SMP) diet and a supra-sustained milk protein (SSMP) diet during an 8-week diet period. A total of seventy-two healthy subjects (31·2 (sd 4·8) kg/m2; 43 (sd 10) years) followed one of the three diets in a subject-specific amount: SMP, SSMP or GMP diet. During weeks 1-4, energy intake was 100 % of individual energy requirement: 10, 40 and 50 % of energy (En %) as protein, fat and carbohydrate, respectively (SMP diet), and 20, 30 and 50 En % as protein, fat and carbohydrate, respectively (SSMP diet or GMP diet). During weeks 5-8, energy intake was 33 % of individual energy requirement: 30, 35 and 35 En % as protein, fat and carbohydrate, respectively (SMP diet), and 60, 5 and 35 En % as protein, fat and carbohydrate, respectively (SSMP diet or GMP diet). Thus, absolute protein intake was kept constant throughout per subject. Significant decreases in BMI (P diets. Decreases in fat-free mass (FFM), fat mass (FM) and FM %, and increases in FFM % were similar between the GMP and both control diets. Changes in RQ differed (P diets. Changes in HDL concentrations differed (P diets ( - 0·08 (sd 0·18) mmol/l and - 0·09 (sd 0·26) mmol/l, respectively). In conclusion, a gelatin-milk protein diet does not induce more beneficial effects during an 8-week weight-loss period compared with a SMP or SSMP diet.

  17. Effects of soybean trypsin inhibitor on hypopharyngeal gland protein content, total midgut protease activity and survival of the honey bee (Apis mellifera L.).

    Science.gov (United States)

    Sagili, Ramesh R; Pankiw, Tanya; Zhu-Salzman, Keyan

    2005-09-01

    Insecticidal properties of protease inhibitors have been established in transgenic plants. In the wake of continuous research and rapid development of protease inhibitors it is important to assess possible effects on beneficial insects like the honey bee (Apis mellifera L.). In this study, newly emerged caged bees were fed pollen diets containing three different concentrations (0.1%, 0.5% and 1% w:w) of soybean trypsin inhibitor (SBTI). Hypopharyngeal gland protein content, total midgut proteolytic enzyme activity of these bees, and survival were measured. Bees fed 1% SBTI had significantly reduced hypopharyngeal gland protein content and midgut proteolytic enzyme activity. There were no significant differences between control, 0.1% and 0.5% SBTI treatments. Bees fed a diet containing 1% SBTI had the lowest survival, followed by 0.5% and 0.1%, over a 30-day period. We concluded that nurse bees fed a pollen diet containing at least 1% SBTI would be poor producers of larval food, potentially threatening colony growth and maintenance.

  18. Construction of a reporter system to study Burkholderia mallei type III secretion and identification of the BopA effector protein function in intracellular survival.

    Science.gov (United States)

    Whitlock, Gregory C; Estes, D Mark; Young, Glenn M; Young, Briana; Torres, Alfredo G

    2008-12-01

    Burkholderia mallei, the aetiological agent of glanders disease, is a Gram-negative facultative intracellular bacterium. Despite numerous studies, the detailed mechanism of its pathogenesis is almost unknown. The presence of a type III secretion system (TTSS) is one of the known mechanisms associated with virulence. An intact TTSS indicates that B. mallei is able to secrete proteins in response to different environmental conditions, which could play an important role in pathogenesis. Therefore, characterization of the TTSS and identification of the secreted proteins associated with bacterial pathogenesis could provide crucial information for the development of a candidate vaccine. In the current study, we used an enzymatic reporter system to establish some of the conditions enabling TTS. Construction of the TTSS bopA mutant revealed that BopA is important for B. mallei invasion and intracellular survival. Overall, our study elucidates how BopA can aid in the optimization of TTS and defines the function of TTS effectors in bacterial intracellular survival and invasion.

  19. Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins

    Science.gov (United States)

    Pellegrin, Clement; Morin, Emmanuelle; Martin, Francis M.; Veneault-Fourrey, Claire

    2015-01-01

    Fungi are major players in the carbon cycle in forest ecosystems due to the wide range of interactions they have with plants either through soil degradation processes by litter decayers or biotrophic interactions with pathogenic and ectomycorrhizal symbionts. Secretion of fungal proteins mediates these interactions by allowing the fungus to interact with its environment and/or host. Ectomycorrhizal (ECM) symbiosis independently appeared several times throughout evolution and involves approximately 80% of trees. Despite extensive physiological studies on ECM symbionts, little is known about the composition and specificities of their secretomes. In this study, we used a bioinformatics pipeline to predict and analyze the secretomes of 49 fungal species, including 11 ECM fungi, wood and soil decayers and pathogenic fungi to tackle the following questions: (1) Are there differences between the secretomes of saprophytic and ECM fungi? (2) Are small-secreted proteins (SSPs) more abundant in biotrophic fungi than in saprophytic fungi? and (3) Are there SSPs shared between ECM, saprotrophic and pathogenic fungi? We showed that the number of predicted secreted proteins is similar in the surveyed species, independently of their lifestyle. The secretome from ECM fungi is characterized by a restricted number of secreted CAZymes, but their repertoires of secreted proteases and lipases are similar to those of saprotrophic fungi. Focusing on SSPs, we showed that the secretome of ECM fungi is enriched in SSPs compared with other species. Most of the SSPs are coded by orphan genes with no known PFAM domain or similarities to known sequences in databases. Finally, based on the clustering analysis, we identified shared- and lifestyle-specific SSPs between saprotrophic and ECM fungi. The presence of SSPs is not limited to fungi interacting with living plants as the genome of saprotrophic fungi also code for numerous SSPs. ECM fungi shared lifestyle-specific SSPs likely involved in

  20. Analyses adjusting for selective crossover show improved overall survival with adjuvant letrozole compared with tamoxifen in the BIG 1-98 study.

    Science.gov (United States)

    Colleoni, Marco; Giobbie-Hurder, Anita; Regan, Meredith M; Thürlimann, Beat; Mouridsen, Henning; Mauriac, Louis; Forbes, John F; Paridaens, Robert; Láng, István; Smith, Ian; Chirgwin, Jacquie; Pienkowski, Tadeusz; Wardley, Andrew; Price, Karen N; Gelber, Richard D; Coates, Alan S; Goldhirsch, Aron

    2011-03-20

    Among postmenopausal women with endocrine-responsive breast cancer, the aromatase inhibitor letrozole, when compared with tamoxifen, has been shown to significantly improve disease-free survival (DFS) and time to distant recurrence (TDR). We investigated whether letrozole monotherapy prolonged overall survival (OS) compared with tamoxifen monotherapy. Of 8,010 postmenopausal women with hormone receptor-positive, early breast cancer enrolled on the Breast International Group (BIG) 1-98 study, 4,922 were randomly assigned to 5 years of continuous adjuvant therapy with either letrozole or tamoxifen. Of 2,459 patients enrolled in the tamoxifen treatment arm, 619 (25.2%) selectively crossed over to either adjuvant or extended letrozole after initial trial results were presented in January 2005. To gain better estimates of relative treatment effects in the presence of selective crossover, we used inverse probability of censoring weighted (IPCW) modeling. Weighted Cox models, by using IPCW, estimated a statistically significant, 18% reduction in the hazard of an OS event with letrozole treatment (hazard ratio [HR], 0.82; 95% CI, 0.70 to 0.95). Estimates of 5-year OS on the basis of IPCW were 91.8% and 90.4% for letrozole and tamoxifen, respectively. The HRs of DFS and TDR events by using IPCW modeling were 0.83 (95% CI, 0.74 to 0.94) and 0.80 (95% CI, 0.67 to 0.94), respectively (P < .05 for DFS, OS, and TDR). Median follow-up was 74 months. Adjuvant treatment with letrozole, compared with tamoxifen, significantly reduces the risk of death, the risk of recurrent disease, and the risk of recurrence at distant sites in postmenopausal women with hormone receptor-positive breast cancer.

  1. Association of rs2282679 A>C polymorphism in vitamin D binding protein gene with colorectal cancer risk and survival: effect modification by dietary vitamin D intake.

    Science.gov (United States)

    Zhu, Yun; Wang, Peizhong Peter; Zhai, Guangju; Bapat, Bharati; Savas, Sevtap; Woodrow, Jennifer R; Campbell, Peter T; Li, Yuming; Yang, Ning; Zhou, Xin; Dicks, Elizabeth; Mclaughlin, John R; Parfrey, Patrick S

    2018-02-06

    The rs2282679 A>C polymorphism in the vitamin D binding protein gene is associated with lower circulating levels of vitamin D. We investigated associations of this SNP with colorectal cancer (CRC) risk and survival and whether the associations vary by dietary vitamin D intake and tumor molecular phenotype. A population-based case-control study identified 637 incident CRC cases (including 489 participants with follow-up data on mortality end-points) and 489 matched controls. Germline DNA samples were genotyped with the Illumina Omni-Quad 1 Million chip in cases and the Affymetrix Axiom® myDesign™ Array in controls. Logistic regression examined the association between the rs2282679 polymorphism and CRC risk with inclusion of potential confounders. Kaplan-Meier curves and multivariable Cox models assessed the polymorphism relative to overall survival (OS) and disease-free survival (DFS). The rs2282679 polymorphism was not associated with overall CRC risk; there was evidence, however, of effect modification by total vitamin D intake (P interaction  = 0.019). Survival analyses showed that the C allele was correlated with poor DFS (per-allele HR, 1.36; 95%CI, 1.05-1.77). The association of rs2282679 on DFS was limited to BRAF wild-type tumors (HR, 1.58; 95%CI, 1.12-2.23). For OS, the C allele was associated with higher all-cause mortality among patients with higher levels of dietary vitamin D (HR, 2.11; 95%CI, 1.29-3.74), calcium (HR, 1.93; 95%CI, 1.08-3.46), milk (HR, 2.36; 95%CI, 1.26-4.44), and total dairy product intakes (HR, 2.03; 95%CI, 1.11-3.72). The rs2282679 SNP was not associated with overall CRC risk, but may be associated with survival after cancer diagnosis. The association of this SNP on survival among CRC patients may differ according to dietary vitamin D and calcium intakes and according to tumor BRAF mutation status.

  2. Differential expression of specific cellular defense proteins in rat hypothalamus under simulated microgravity induced conditions: comparative proteomics.

    Science.gov (United States)

    Iqbal, Javed; Li, Wang; Hasan, Murtaza; Liu, Kefu; Awan, Umer; Saeed, Yasmeen; Zhang, Yongqian; Muhammad Khan, Arif; Shah, Amin; Qing, Hong; Deng, Yulin

    2014-06-01

    Microgravity severely halts the structural and functional cerebral capacity of astronauts especially affecting their brains due to the stress produced by cephalic fluid shift. We employed a rat tail suspension model to substantiate simulated microgravity (SM) in brain. In this study, comparative mass spectrometry was applied in order to demonstrate the differential expression of 17 specific cellular defense proteins. Gamma-enolase, peptidyl-prolyl cis-trans isomerase A, glial fibrillary acidic protein, heat shock protein HSP 90-alpha, 10 kDa heat shock protein, mitochondrial, heat shock cognate 71 kDa protein, superoxide dismutase 1 and dihydropyrimidinase-related protein 2 were found to be upregulated by HPLC/ESI-TOF. Furthermore, five differentially expressed proteins including 60 kDa heat shock protein, mitochondrial, heat shock protein HSP 90-beta, peroxiredoxin-2, stress-induced-phosphoprotein, and UCHL-1 were found to be upregulated by HPLC/ESI-Q-TOF MS. In addition, downregulated proteins include cytochrome C, superoxide dismutase 2, somatic, and excitatory amino acid transporter 1 and protein DJ-1. Validity of MS results was successfully performed by Western blot analysis of DJ-1 protein. This study will not only help to understand the neurochemical responses produced under microgravity but also will give future direction to cure the proteomic losses and their after effects in astronauts. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. The Olive Oil-Based Lipid Clinoleic Blocks Leukocyte Recruitment and Improves Survival during Systemic Inflammation: A Comparative In Vivo Study of Different Parenteral Lipid Emulsions

    Directory of Open Access Journals (Sweden)

    Kirsten Buschmann

    2015-01-01

    Full Text Available Although fish oil-based and olive oil-based lipid emulsions have been shown to exert anti-inflammatory functions, the immunomodulating properties of lipids are still controversial. Therefore, we investigated the anti-inflammatory effect of three different parenterally administered lipid emulsions in vivo: olive oil-based Clinoleic, fish oil-based Smoflipid, and soybean oil-based Lipofundin. We observed leukocyte recruitment in inflamed murine cremaster muscle using intravital microscopy and survival in a murine model of LPS-induced systemic inflammation and analyzed expression of leukocyte and endothelial adhesion molecules. Olive oil-based Clinoleic and fish oil-based Smoflipid profoundly inhibited leukocyte adhesion compared to Lipofundin during LPS-induced inflammation of the murine cremaster muscle. In the trauma model of cremaster muscle inflammation, Lipofundin was the only lipid emulsion that even augmented leukocyte adhesion. In contrast to Smoflipid and Lipofundin, Clinoleic effectively blocked leukocyte recruitment and increased survival during lethal endotoxemia. Flow chamber experiments and analysis of adhesion molecule expression suggest that both endothelial and leukocyte driven mechanisms might contribute to anti-inflammatory effects of Clinoleic. We conclude that the anti-inflammatory properties of Clinoleic are superior to those of Smoflipid and Lipofundin even during systemic inflammation. Thus, these results should stimulate further studies investigating parenteral lipids as an anti-inflammatory strategy in critically ill patients.

  4. The olive oil-based lipid clinoleic blocks leukocyte recruitment and improves survival during systemic inflammation: a comparative in vivo study of different parenteral lipid emulsions.

    Science.gov (United States)

    Buschmann, Kirsten; Poeschl, Johannes; Braach, Natascha; Hudalla, Hannes; Kuss, Navina; Frommhold, David

    2015-01-01

    Although fish oil-based and olive oil-based lipid emulsions have been shown to exert anti-inflammatory functions, the immunomodulating properties of lipids are still controversial. Therefore, we investigated the anti-inflammatory effect of three different parenterally administered lipid emulsions in vivo: olive oil-based Clinoleic, fish oil-based Smoflipid, and soybean oil-based Lipofundin. We observed leukocyte recruitment in inflamed murine cremaster muscle using intravital microscopy and survival in a murine model of LPS-induced systemic inflammation and analyzed expression of leukocyte and endothelial adhesion molecules. Olive oil-based Clinoleic and fish oil-based Smoflipid profoundly inhibited leukocyte adhesion compared to Lipofundin during LPS-induced inflammation of the murine cremaster muscle. In the trauma model of cremaster muscle inflammation, Lipofundin was the only lipid emulsion that even augmented leukocyte adhesion. In contrast to Smoflipid and Lipofundin, Clinoleic effectively blocked leukocyte recruitment and increased survival during lethal endotoxemia. Flow chamber experiments and analysis of adhesion molecule expression suggest that both endothelial and leukocyte driven mechanisms might contribute to anti-inflammatory effects of Clinoleic. We conclude that the anti-inflammatory properties of Clinoleic are superior to those of Smoflipid and Lipofundin even during systemic inflammation. Thus, these results should stimulate further studies investigating parenteral lipids as an anti-inflammatory strategy in critically ill patients.

  5. A specific inhibitor of protein kinase CK2 delays gamma-H2Ax foci removal and reduces clonogenic survival of irradiated mammalian cells

    Directory of Open Access Journals (Sweden)

    Huber Peter E

    2011-02-01

    Full Text Available Abstract Background The protein kinase CK2 sustains multiple pro-survival functions in cellular DNA damage response and its level is tightly regulated in normal cells but elevated in cancers. Because CK2 is thus considered as potential therapeutic target, DNA double-strand break (DSB formation and rejoining, apoptosis induction and clonogenic survival was assessed in irradiated mammalian cells upon chemical inhibition of CK2. Methods MRC5 human fibroblasts and WIDR human colon carcinoma cells were incubated with highly specific CK2 inhibitor 4,5,6,7-tetrabromobenzotriazole (TBB, or mock-treated, 2 hours prior to irradiation. DSB was measured by pulsed-field electrophoresis (PFGE as well as gamma-H2AX foci formation and removal. Apoptosis induction was tested by DAPI staining and sub-G1 flow cytometry, survival was quantified by clonogenic assay. Results TBB treatment did not affect initial DNA fragmention (PFGE; up to 80 Gy or foci formation (1 Gy. While DNA fragment rejoining (PFGE was not inhibited by the drug, TBB clearly delayed gamma-H2AX foci disappearence during postirradiation incubation. No apoptosis induction could be detected for up to 38 hours for both cell lines and exposure conditions (monotherapies or combination, but TBB treatment at this moderately toxic concentration of 20 μM (about 40% survival enhanced radiation-induced cell killing in the clonogenic assay. Conclusions The data imply a role of CK2 in gamma-H2AX dephosporylation, most likely through its known ability to stimulate PP2A phosphatase, rather than DSB rejoining. The slight but definite clonogenic radiosensitization by TBB does apparently not result from interference with an apoptosis suppression function of CK2 in these cells but could reflect inhibitor-induced uncoupling of DNA damage response decay from break ligation.

  6. Comparative characterization of proteins secreted by Neurospora sitophila in solid-state and submerged fermentation.

    Science.gov (United States)

    Li, Yanjun; Peng, Xiaowei; Chen, Hongzhang

    2013-10-01

    Although submerged fermentation (SmF) accounts for most of current enzyme industries, it has been reported that solid-state fermentation (SSF) can produce higher enzyme yields in laboratory scale. In order to understand the reasons contributing to high enzyme production in SSF, this study compared the cellulase activities and secretomes of Neurospora sitophila cultured in SSF and SmF using steam exploded wheat straw as carbon source and enzyme inducer. The total amounts of protein and biomass (glucosamine content) in SSF were respectively 30 and 2.8 times of those in SmF. The CMCase, FPA and β-glucoside activities in SSF were 53-181 times of those in SmF. Both in SSF and SmF, N. sitophila secreted the most critical cellulases and hemicellulases known for Trichoderma reesei, although a β-xylosidase was exclusively identified in SSF. Six endoglucanases were identified in N. sitophila secretion with the high CMCase activity. The non-enzyme proteins in SSF were involved in fungal mycelia growth and conidiation; while those in SmF were more related to glycometabolism and stress tolerance. This revealed that SSF more likely serves as a natural habitat for filamentous fungi to facilitate the enzyme secretion. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  7. Comparative sequence analysis of the non-protein-coding mitochondrial DNA of inbred rat strains.

    Science.gov (United States)

    Abhyankar, Avinash; Park, Hee-Bok; Tonolo, Giancarlo; Luthman, Holger

    2009-12-07

    The proper function of mammalian mitochondria necessitates a coordinated expression of both nuclear and mitochondrial genes, most likely due to the co-evolution of nuclear and mitochondrial genomes. The non-protein coding regions of mitochondrial DNA (mtDNA) including the D-loop, tRNA and rRNA genes form a major component of this regulated expression unit. Here we present comparative analyses of the non-protein-coding regions from 27 Rattus norvegicus mtDNA sequences. There were two variable positions in 12S rRNA, 20 in 16S rRNA, eight within the tRNA genes and 13 in the D-loop. Only one of the three neutrality tests used demonstrated statistically significant evidence for selection in 16S rRNA and tRNA-Cys. Based on our analyses of conserved sequences, we propose that some of the variable nucleotide positions identified in 16S rRNA and tRNA-Cys, and the D-loop might be important for mitochondrial function and its regulation.

  8. Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations.

    Science.gov (United States)

    Wirth, Anna Jean; Liu, Yanxin; Prigozhin, Maxim B; Schulten, Klaus; Gruebele, Martin

    2015-06-10

    The unimolecular folding reaction of small proteins is now amenable to a very direct mechanistic comparison between experiment and simulation. We present such a comparison of microsecond pressure and temperature jump refolding kinetics of the engineered WW domain FiP35, a model system for β-sheet folding. Both perturbations produce experimentally a faster and a slower kinetic phase, and the "slow" microsecond phase is activated. The fast phase shows differences between perturbation methods and is closer to the downhill limit by temperature jump, but closer to the transiently populated intermediate limit by pressure jump. These observations make more demands on simulations of the folding process than just a rough comparison of time scales. To complement experiments, we carried out several pressure jump and temperature jump all-atom molecular dynamics trajectories in explicit solvent, where FiP35 folded in five of the six simulations. We analyzed our pressure jump simulations by kinetic modeling and found that the pressure jump experiments and MD simulations are most consistent with a 4-state kinetic mechanism. Together, our experimental and computational data highlight FiP35's position at the boundary where activated intermediates and downhill folding meet, and we show that this model protein is an excellent candidate for further pressure jump molecular dynamics studies to compare experiment and modeling at the folding mechanism level.

  9. Adeno-Associated Virus (AAV) Type 5 Rep Protein Cleaves a Unique Terminal Resolution Site Compared with Other AAV Serotypes

    OpenAIRE

    Chiorini, John A.; Afione, Sandra; Kotin, Robert M

    1999-01-01

    Adeno-associated virus (AAV) replication depends on two viral components for replication: the AAV nonstructural proteins (Rep) in trans, and inverted terminal repeat (ITR) sequences in cis. AAV type 5 (AAV5) is a distinct virus compared to the other cloned AAV serotypes. Whereas the Rep proteins and ITRs of other serotypes are interchangeable and can be used to produce recombinant viral particles of a different serotype, AAV5 Rep proteins cannot cross-complement in the packaging of a genome w...

  10. A systematic review of human norovirus survival reveals a greater persistence of human norovirus RT-qPCR signals compared to those of cultivable surrogate viruses.

    Science.gov (United States)

    Knight, Angus; Haines, John; Stals, Ambroos; Li, Dan; Uyttendaele, Mieke; Knight, Alastair; Jaykus, Lee-Ann

    2016-01-04

    Human noroviruses (hNoV) are the single largest cause of acute gastroenteritis in the western world. The efficacy of hNoV control measures remains largely unknown, partly owing to the inability to grow the virus in vitro and partly to the large number of surrogate studies of unknown relevance. A systematic review of the persistence and survival of hNoV in foods and the environment was undertaken based upon PRISMA (preferred reporting items for systematic reviews and meta analyses) guidelines to answer the questions: (1) "What are the natural hNoV persistence characteristics in food and the environment?" and (2) "How can these properties be altered by applying physical and/or chemical treatments to foods or food contact surfaces?" Over 10,000 citations were screened using defined inclusion and exclusion criteria. One hundred and twenty-six (126) citations were identified for further evaluation and data were extracted based upon the conditions of study and treatment (e.g., treatment parameters, pH, and temperature, time, infectivity, and RT-qPCR results). Since the only markers for hNoV persistence and survival were RT-qPCR data and human challenge studies, citations for further analysis were restricted to only those that included data on hNoV behavior (using RT-qPCR) as compared directly to surrogate virus behavior (using both RT-qPCR and infectivity) in the same study, and clinical studies. Based on these criteria, a total of 12 independent studies (5 for thermal inactivation and 7 for available chlorine) and 3 human challenge studies were identified. RT-qPCR always underestimated reductions in surrogate virus titre as a function of treatment when compared to infectivity. The corresponding reductions in RT-qPCR signals for hNoV under comparable conditions were nearly always less than those observed for the surrogates. These relationships were statistically significant for heat when comparing persistence of hNoV RT-qPCR signals with surrogate MNV-1 RT-qPCR signals

  11. Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins.

    Science.gov (United States)

    Pabuwal, Vagmita; Li, Zhijun

    2009-02-01

    Elucidating the distinct topology of residue packing in transmembrane proteins is essential for developing high-quality computational tools for their structure prediction. Network approaches transforming a protein's three-dimensional structure into a network have proven useful in analyzing various aspects of protein structures. Residues with high degree of connectivity as identified through network analysis are considered to be important for the stability of a protein's folded structure. It is thus of interest to study the packing topology of these structurally important residues in membrane proteins. In this work, we systematically characterized the importance and the spatial topology of these highly connected residues in helical membrane and helical soluble proteins from several aspects. A representative helical membrane protein and two helical soluble protein structure data sets were compiled and analyzed. Results of analyses indicate that the highly connected amino acid residues in membrane proteins are more scattered peripherally and more exposed to the membrane than in soluble proteins. Accordingly, they are less densely connected with each other in membrane proteins than in soluble proteins. Together with the knowledge of a centralized function site for many membrane proteins, these findings suggest a structure-function model that is distinguishable from soluble proteins.

  12. Survival time and stability properties of disease-associated prion protein in chronic wasting disease of elk

    Science.gov (United States)

    Background: The Rocky Mountain elk (Cervus elaphus nelsoni) prion protein gene exhibits amino acid polymorphism at codon 132, with 132L (leucine) and 132M (methionine) allelic variants present in the population. We have previously shown that following experimental oral challenge with chronic wasting...

  13. Comparative Analysis of the Proteins with Tandem Repeats from 8 Microsporidia and Characterization of a Novel Endospore Wall Protein Colocalizing with Polar Tube from Nosema bombycis.

    Science.gov (United States)

    Wang, Ying; Geng, Huixia; Dang, Xiaoqun; Xiang, Heng; Li, Tian; Pan, Guoqing; Zhou, Zeyang

    2017-09-01

    As a common feature of eukaryotic proteins, tandem amino acid repeat has been studied extensively in both animal and plant proteins. Here, a comparative analysis focusing on the proteins having tandem repeats was conducted in eight microsporidia, including four mammal-infecting microsporidia (Encephalitozoon cuniculi, Encephalitozoon intestinalis, Encephalitozoon hellem and Encephalitozoon bieneusi) and four insect-infecting microsporidia (Nosema apis, Nosema ceranae, Vavraia culicis and Nosema bombycis). We found that the proteins with tandem repeats were abundant in these species. The quantity of these proteins in insect-infecting microsporidia was larger than that of mammal-infecting microsporidia. Additionally, the hydrophilic residues were overrepresented in the tandem repeats of these eight microsporidian proteins and the amino acids residues in these tandem repeat sequences tend to be encoded by GC-rich codons. The tandem repeat position within proteins of insect-infecting microsporidia was randomly distributed, whereas the tandem repeats within proteins of mammal-infecting microsporidia rarely tend to be present in the N terminal regions, when compared with those present in the C terminal and middle regions. Finally, a hypothetical protein EOB14572 possessing four tandem repeats was successfully characterized as a novel endospore wall protein, which colocalized with polar tube of N. bombycis. Our study provided useful insight for the study of the proteins with tandem repeats in N. bombycis, but also further enriched the spore wall components of this obligate unicellular eukaryotic parasite. © 2017 The Author(s) Journal of Eukaryotic Microbiology © 2017 International Society of Protistologists.

  14. Rainbow trout surviving infections of viral haemorrhagic septicemia virus (VHSV) show lasting antibodies to recombinant G protein fragments

    DEFF Research Database (Denmark)

    Encinas, P.; Gomez-Casado, E.; Grandes, Fregeneda

    2011-01-01

    sera from trout infected with the homologous VHSV isolate but also with the VHSV-DK-201433 heterologous isolate, which had 13 amino acid changes. Sera from healthy trout and/or from trout surviving infectious haematopoietic necrosis virus (IHNV) infection, were used to calculate cut-off absorbances...... refinements of the frg-ELISA could allow detection of anti-VHSV trout Abs in natural outbreaks caused by different heterologous VHSV isolates. The homologous frg-ELISA method could be useful to follow G immunization attempts during vaccine development and/or to best understand the fish Ab response during VHSV...... infections. The viral frgs approach might also be used with other fish species and/or viruses....

  15. Metabolic and protein interaction sub-networks controlling the proliferation rate of cancer cells and their impact on patient survival.

    Science.gov (United States)

    Feizi, Amir; Bordel, Sergio

    2013-10-24

    Cancer cells can have a broad scope of proliferation rates. Here we aim to identify the molecular mechanisms that allow some cancer cell lines to grow up to 4 times faster than other cell lines. The correlation of gene expression profiles with the growth rate in 60 different cell lines has been analyzed using several genome-scale biological networks and new algorithms. New possible regulatory feedback loops have been suggested and the known roles of several cell cycle related transcription factors have been confirmed. Over 100 growth-correlated metabolic sub-networks have been identified, suggesting a key role of simultaneous lipid synthesis and degradation in the energy supply of the cancer cells growth. Many metabolic sub-networks involved in cell line proliferation appeared also to correlate negatively with the survival expectancy of colon cancer patients.

  16. Decreased cytoplasmic X-box binding protein-1 expression is associated with poor prognosis and overall survival in patients with oral squamous cell carcinoma.

    Science.gov (United States)

    Hsu, Hui-Ting; Hsing, Ming-Tai; Yeh, Chung-Min; Chen, Chih-Jung; Yang, Jia-Sin; Yeh, Kun-Tu

    2018-01-02

    Squamous cell carcinoma is the most common cancer of the oral cavity. In spite of advancements in surgical, chemoradiological and targeted therapies, these therapeutic strategies still have had little impact on survival rates. X-box binding protein-1 (XBP-1) is a potent transcription factor that is involved in the unfolded protein response (UPR) pathway, which itself is activated in response to endoplasmic reticulum stress as a method to restore cellular homeostasis. The role XBP-1 plays in oral squamous cell carcinoma (OSCC) has yet to be determined. In this study, we used molecular and immunohistochemical analyses to investigate the role of XBP-1 protein playing in the OSCC carcinogenesis. We used immunohistochemical analyses to investigate XBP-1 expression in 255 OSCC tissue specimens, as well as migration and invasion assays with XBP-1 siRNA transfection of oral cancer cell lines to confirm its role in OSCC. The XBP-1 immunostaining was dichotomized as low-level expression and high-level expression. We found that low-level cytoplasmic XBP-1expression was significantly correlated with larger tumor size (p=0.047), more advanced clinical stage (pCox regression analysis revealed that cytoplasmic XBP-1 expression was a prognostic factor for overall survival of patients with OSCC. We also found that inhibition of XBP-1 promoted OSCC cell migration and invasion. Our results suggest that XBP-1 expression may play an essential role in the pathogenesis of OSCC and that targeting XBP-1 may be a sound therapeutic strategy. Copyright © 2018 Elsevier B.V. All rights reserved.

  17. Genome-wide comparative analysis of tonoplast intrinsic protein (TIP) genes in plants.

    Science.gov (United States)

    Regon, Preetom; Panda, Piyalee; Kshetrimayum, Erina; Panda, Sanjib Kumar

    2014-12-01

    Tonoplast intrinsic proteins (TIPs) play a vital role in water transport across membranes. In the present study, we performed a comparative analysis of TIP genes in ten plant species including both monocots and dicots. A total of 100 TIP aquaporin genes were identified, and their relationships among the plant species were analyzed. Phylogenetic analysis was performed to evaluate the relationship of these genes within the plant species. Based on the phylogenetic analysis results, TIPs were classified into five distinct arbitrary groups (group I to group V), which represented TIP2, TIP5, TIP4, TIP1, and TIP3, respectively. Group I represented the largest arbitrary group, followed by group IV, in the phylogenetic tree. The result clearly indicates that TIP2 and TIP1 are abundant aquaporins and highly related among the species. In the present review, a comparative study of gene structure analysis between dicots and monocots has been performed to analyze their structural variation. Most of the predicted motifs are conserved among the species, signifying an evolutionary relationship. The gene expression analysis indicated that the expression of TIP genes varies during different developmental stages and also during stressed conditions. The results indicated a great degree of evolutionary relationship and variation in the expression levels of TIPs in plants.

  18. Soy Flour Adhesive Strength Compared with That of Purified Soy Proteins*

    Science.gov (United States)

    Linda Lorenz; Michael Birkeland; Chera Daurio; Charles R. Frihart

    2015-01-01

    Except for the substitution of soy flour in phenolic resins (Frihart et al. 2013) and the use of soy flour at high pHs (Lambuth 2003), the literature on soy protein properties for adhesives has mainly focused on soy protein isolate and specific protein fractions (Sun 2005b). The assumption is that proteins are the main portion of soy flour giving bond strength and the...

  19. Comparative Proteomics Provides Insights into Metabolic Responses in Rat Liver to Isolated Soy and Meat Proteins

    NARCIS (Netherlands)

    Song, Shangxin; Hooiveld, G.J.E.J.; Zhang, W.; Li, Mengjie; Zhoa, Fan; Xu, Xinglian; Müller, M.R.; Li, Chunbao; Zhou, Guanghong

    2016-01-01

    It has been reported that isolated dietary soy and meat proteins have distinct effects on physiology and liver gene expression, but the impact on protein expression responses are unknown. Because these may differ from gene expression responses, we investigated dietary protein-induced changes in

  20. Comparative Proteomic Analysis of Two Barley Cultivars (Hordeum vulgare L.) with Contrasting Grain Protein Content

    Science.gov (United States)

    Guo, Baojian; Luan, Haiye; Lin, Shen; Lv, Chao; Zhang, Xinzhong; Xu, Rugen

    2016-01-01

    Grain protein contents (GPCs) of barley seeds are significantly different between feed and malting barley cultivars. However, there is still no insight into the proteomic analysis of seed proteins between feed and malting barley cultivars. Also, the genetic control of barley GPC is still unclear. GPCs were measured between mature grains of Yangsimai 3 and Naso Nijo. A proteome profiling of differentially expressed protein was established by using a combination of 2-DE and tandem mass spectrometry. In total, 502 reproducible protein spots in barley seed proteome were detected with a pH range of 4–7 and 6–11, among these 41 protein spots (8.17%) were detected differentially expressed between Yangsimai 3 and Naso Nijo. Thirty-four protein spots corresponding to 23 different proteins were identified, which were grouped into eight categories, including stress, protein degradation and post-translational modification, development, cell, signaling, glycolysis, starch metabolism, and other functions. Among the identified proteins, enolase (spot 274) and small subunit of ADP-glucose pyrophosphorylase (spot 271) are exclusively expressed in barley Yangsimai 3, which may be involved in regulating seed protein expression. In addition, malting quality is characterized by an accumulation of serpin protein, Alpha-amylase/trypsin inhibitor CMb and Alpha-amylase inhibitor BDAI-1. Most noticeably, globulin, an important storage protein in barley seed, undergoes post-translational processing in both cultivars, and also displays different expression patterns. PMID:27200019

  1. Comparative and functional analysis of the widely occurring family of Nep1-like proteins

    NARCIS (Netherlands)

    Oome, Stan|info:eu-repo/dai/nl/325800847; van den Ackerveken, Guido|info:eu-repo/dai/nl/113853254

    2014-01-01

    Nep1-like proteins (NLP) are best known for their cytotoxic activity in dicot plants. NLP are taxonomically widespread among microbes with very different lifestyles. To learn more about this enigmatic protein family, we analyzed more than 500 available NLP protein sequences from fungi, oomycetes,

  2. The G protein-coupled estrogen receptor 1 (GPER/GPR30 does not predict survival in patients with ovarian cancer

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    Kolkova Zuzana

    2012-03-01

    Full Text Available Abstract Background Even though ovarian tumors are not generally considered estrogen-sensitive, estrogens may still have an impact on ovarian tumor progression. The recently identified trans-membrane estrogen receptor GPER is involved in rapid estrogen signaling. Furthermore, it binds selective estrogen receptor modulators with agonistic effect, which could explain tamoxifen controversies. Methods GPER mRNA was assayed with quantitative real-time PCR (qPCR in 42 primary ovarian tumors and 7 ovarian cancer cell lines. ERα and ERβ mRNA were analyzed for comparison. GPER protein was semi-quantified with densitometric scanning of Western blots and its tissue distribution analyzed with immunohistochemistry (IHC in 40 ovarian tumors. In addition, IHC was evaluated in a tissue microarray (TMA of 150 primary malignant ovarian tumors. Results All tumor samples contained GPER mRNA. The content of mRNA was not different between benign and malignant tumors, but one third of malignant samples over-expressed GPER mRNA. The content of ERα mRNA was higher in malignant than in benign tumors, whereas ERβ mRNA was higher in benign than in malignant tumors. GPER mRNA was detected in all seven ovarian cancer cell lines with highest levels in TOV21G and TOV112D cells. Similar expression pattern was seen for ERβ mRNA. Western blot demonstrated GPER protein in all tumor samples. Semi-quantification showed no difference between benign and malignant tumors, but about one third of malignant samples over-expressed GPER protein. GPER staining was localized mainly in epithelial cells. In the TMA study we found no correlation between GPER staining and clinical stage, histological grade or patient survival. Conclusions GPER mRNA as well as GPER protein is present in both benign and malignant ovarian tumor tissue. About one third of malignant tumors over-expressed both GPER mRNA and protein. This, however, correlated neither with histological or clinical parameters nor

  3. HuD and the Survival Motor Neuron Protein Interact in Motoneurons and Are Essential for Motoneuron Development, Function, and mRNA Regulation.

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    Hao le, Thi; Duy, Phan Q; An, Min; Talbot, Jared; Iyer, Chitra C; Wolman, Marc; Beattie, Christine E

    2017-11-29

    Motoneurons establish a critical link between the CNS and muscles. If motoneurons do not develop correctly, they cannot form the required connections, resulting in movement defects or paralysis. Compromised development can also lead to degeneration because the motoneuron is not set up to function properly. Little is known, however, regarding the mechanisms that control vertebrate motoneuron development, particularly the later stages of axon branch and dendrite formation. The motoneuron disease spinal muscular atrophy (SMA) is caused by low levels of the survival motor neuron (SMN) protein leading to defects in vertebrate motoneuron development and synapse formation. Here we show using zebrafish as a model system that SMN interacts with the RNA binding protein (RBP) HuD in motoneurons in vivo during formation of axonal branches and dendrites. To determine the function of HuD in motoneurons, we generated zebrafish HuD mutants and found that they exhibited decreased motor axon branches, dramatically fewer dendrites, and movement defects. These same phenotypes are present in animals expressing low levels of SMN, indicating that both proteins function in motoneuron development. HuD binds and transports mRNAs and one of its target mRNAs, Gap43, is involved in axonal outgrowth. We found that Gap43 was decreased in both HuD and SMN mutants. Importantly, transgenic expression of HuD in motoneurons of SMN mutants rescued the motoneuron defects, the movement defects, and Gap43 mRNA levels. These data support that the interaction between SMN and HuD is critical for motoneuron development and point to a role for RBPs in SMA.SIGNIFICANCE STATEMENT In zebrafish models of the motoneuron disease spinal muscular atrophy (SMA), motor axons fail to form the normal extent of axonal branches and dendrites leading to decreased motor function. SMA is caused by low levels of the survival motor neuron (SMN) protein. We show in motoneurons in vivo that SMN interacts with the RNA binding

  4. Computational Studies of the Structural Stability of Rabbit Prion Protein Compared to Human and Mouse Prion Proteins

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    Zhang, Jiapu

    2011-01-01

    Prion diseases are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. The neurodegenerative diseases such as Creutzfeldt-Jakob disease, variant Creutzfeldt-Jakob diseases, Gerstmann-Str$\\ddot{a}$ussler-Scheinker syndrome, Fatal Familial Insomnia, Kuru in humans, scrapie in sheep, bovine spongiform encephalopathy (or 'mad-cow' disease) and chronic wasting disease in cattle belong to prion diseases. By now there have not been some effective therapeutic approaches to treat all these prion diseases. Dogs, rabbits and horses were reported to be resistant to prion diseases. By the end of year 2010 all the NMR structures of dog, rabbit and horse prion proteins (X-ray for rabbits too) had been finished to release into protein data bank. Thus, at this moment it is very worth studying the NMR and X-ray molecular structures of horse, dog and rabbit prion proteins to obtain insights into their immunity prion diseases. The author found that dog and horse prion proteins have sta...

  5. A comparative study of protein synthesis in in vitro systems: from the prokaryotic reconstituted to the eukaryotic extract-based

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    Hillebrecht Jason R

    2008-07-01

    Full Text Available Abstract Background Cell-free protein synthesis is not only a rapid and high throughput technology to obtain proteins from their genes, but also provides an in vitro platform to study protein translation and folding. A detailed comparison of in vitro protein synthesis in different cell-free systems may provide insights to their biological differences and guidelines for their applications. Results Protein synthesis was investigated in vitro in a reconstituted prokaryotic system, a S30 extract-based system and a eukaryotic system. Compared to the S30 system, protein synthesis in the reconstituted system resulted in a reduced yield, and was more cold-sensitive. Supplementing the reconstituted system with fractions from a size-exclusion separation of the S30 extract significantly increased the yield and activity, to a level close to that of the S30 system. Though protein synthesis in both prokaryotic and eukaryotic systems showed no significant differences for eukaryotic reporter proteins, drastic differences were observed when an artificial fusion protein was synthesized in vitro. The prokaryotic systems failed to synthesize and correctly fold a significant amount of the full-length fusion protein, even when supplemented with the eukaryotic lysate. The active full-length fusion protein was synthesized only in the eukaryotic system. Conclusion The reconstituted bacterial system is sufficient but not efficient in protein synthesis. The S30 system by comparison contains additional cellular factors capable of enhancing protein translation and folding. The eukaryotic translation machinery may have evolved from its prokaryotic counterpart in order to translate more complex (difficult-to-translate templates into active proteins.

  6. An anthraquinone derivative, emodin sensitizes hepatocellular carcinoma cells to TRAIL induced apoptosis through the induction of death receptors and downregulation of cell survival proteins.

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    Subramaniam, Aruljothi; Loo, Ser Yue; Rajendran, Peramaiyan; Manu, Kanjoormana A; Perumal, Ekambaram; Li, Feng; Shanmugam, Muthu K; Siveen, Kodappully Sivaraman; Park, Joo-In; Ahn, Kwang Seok; Hui, Kam M; Kumar, Alan P; Sethi, Gautam

    2013-10-01

    Recombinant tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is currently under clinical trials for cancer, however many tumor cells, including hepatocellular carcinoma (HCC) develop resistance to TRAIL-induced apoptosis. Hence, novel agents that can alleviate TRAIL-induced resistance are urgently needed. In the present report, we investigated the potential of emodin to enhance apoptosis induced by TRAIL in HCC cells. As observed by MTT cytotoxicity assay and the externalization of the membrane phospholipid phosphatidylserine, we found that emodin can significantly potentiate TRAIL-induced apoptosis in HCC cells. When investigated for the mechanism(s), we observed that emodin can downregulate the expression of various cell survival proteins, and induce the cell surface expression of both TRAIL receptors, death receptors (DR) 4 as well as 5. In addition, emodin increased the expression of C/EBP homologous protein (CHOP) in a time-dependent manner. Knockdown of CHOP by siRNA decreased the induction of emodin-induced DR5 expression and apoptosis. Emodin-induced induction of DR5 was mediated through the generation of reactive oxygen species (ROS), as N-acetylcysteine blocked the induction of DR5 and the induction of apoptosis. Also, the knockdown of X-linked inhibitor of apoptosis protein by siRNA significantly reduced the sensitization effect of emodin on TRAIL-induced apoptosis. Overall, our experimental results clearly indicate that emodin can indeed potentiate TRAIL-induced apoptosis through the downregulation of antiapoptotic proteins, increased expression of apoptotic proteins, and ROS mediated upregulation of DR in HCC cells.

  7. Comparative study of heparin-binding proteins profile of Murrah buffalo (Bubalus bubalis semen

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    S. S. Ramteke

    2014-09-01

    Full Text Available Aim: The experiment was conducted to study the total seminal plasma protein (TSPP and heparin-binding proteins (HBPs in relation to initial semen quality of buffalo bull. Materials and Methods: Semen from two Murrah buffalo bulls (bull no. 605 and 790 with mass motility of ≥3+ were used for the study and categorized into three groups (Group I- Mass motility 3+, Group II- Mass motility 4+ and Group III- Mass motility 5+. Seminal plasma from semen was separated by centrifugation. HBPs was isolated and purified from heparin-agarose affinity column by modified elution buffer. TSPP and isolated HBPs concentration was estimated by Lowry’s method. The purified HBPs were resolved on Sodium dodecyl sulfate polyacrylamide gel electrophoresis to check the protein profile of two bulls. Results: The mean values of TSPP concentrations in bull no. 605 and 790 in Group I, II and III were 30.64±0.12, 31.66±0.09, 32.53±0.19 and 28.51±0.09, 29.49±0.15, 30.45±0.17 mg/mL, respectively. The mean values of HBPs concentrations in bull no. 605 and 790 in Group I, II and III were 3.11±0.07, 3.32±0.06, 3.46±0.08 and 2.51±0.08, 2.91±0.05, 3.10±0.03 mg/mL, respectively. Both the values of TSPP and HBPs were significantly higher (p<0.01 in bull no. 605 when compared to 790 in all the three groups. 31 kDa HBP was more intensely present in bull no. 605, thus may indicate its superiority over bull no. 790 in relation to fertility potential. Conclusion: TSPP and HBPs shows variation in concentration with respect to initial semen quality. Furthermore, presence of fertility related 31 kDa HBPs in one of the bull may be an indication of high fertility of a bull. In future, in-vivo and in-vitro correlative study on larger basis is needed for the establishment of fertility-related HBPs in semen which might establish criteria for selection of buffalo bull with high fertility potential.

  8. Overexpression of MDM2 protein in ameloblastomas as compared to adenomatoid odontogenic tumor

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    A Krishna

    2012-01-01

    Full Text Available Background: Recent studies on odontogenic tumors have identified various molecular alterations responsible for their development, and determination of epithelial proliferation is a useful means of investigating the differences in biologic behavior of these tumors. One such specific marker to identify proliferative activity and tumor aggressiveness by immunohistochemistry (IHC is MDM2, 90-95kDa protein. Objective: This immunohistochemical study using MDM2 expression was undertaken to understand better the diverse biological activity of two groups of odontogenic tumors namely ameloblastoma and adenomatoid odontogenic tumor (AOT based on their cell proliferation activity. Materials and Methods: A total of 50 cases, comprising of 36 ameloblastoma samples and 14 AOT samples, were subjected to heat-induced antigen retrieval method using citrate buffer in a pressure cooker. Consequently, the sections were stained with MDM2 monoclonal antibody and visualized using an LSAB+ kit. Results: In ameloblastomas, statistically significant association was seen between plexiform ameloblastomas, follicular ameloblastomas with granular cell changes, desmoplastic and unicystic variants. The predominant nuclear staining by MDM2 revealed overexpression in ameloblastomas as compared to AOT. Conclusion: The MDM2 overexpression noticed in plexiform ameloblastoma, follicular ameloblastoma with granular cell changes and acanthomatous ameloblastoma when compared to simple unicystic and desmoplastic ameloblastoma suggest a relatively enhanced proliferative phenotype of these solid multicystic variants of ameloblastomas. On overall comparison, higher expression was noted in ameloblastomas when compared to AOT. This indicates differences in the aggressive nature between these two groups of odontogenic tumors favoring the perception of a greater aggressive nature of ameloblastomas.

  9. Elevated ZNF703 Protein Expression Is an Independent Unfavorable Prognostic Factor for Survival of the Patients with Head and Neck Squamous Cell Carcinoma

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    Hang Yang

    2015-01-01

    Full Text Available Aim. Data from The Cancer Genome Atlas (TCGA show that the ZNF703 gene amplifies and overexpresses in head and neck squamous cell carcinomas (HNSCC. However, the clinical relevance of this observation in HNSCC is unclear. The purpose of this study was to clarify the expression of ZNF703 protein and its prognostic effect on HNSCC. Methods. Two hundred ten HNSCC patients from Sun Yat-Sen University Cancer Center with complete survival follow-up were included in this study. Tumor samples from primary sites were collected. The expression of the ZNF703 protein was tested by immunohistochemistry (IHC. Results. The high expression of ZNF703 in HNSCC tumor tissues was significantly higher than that of the matched noncancerous tissues (48.6% versus 11.6%, P<0.001. ZNF703 overexpression was correlated with tumor position (laryngeal carcinoma and recurrence (all P<0.05. Multivariate analysis revealed that ZNF703 protein overexpression was an independent prognostic factor (P=0.022, hazard ratio = 1.635, 95% CI 1.073–2.493 in HNSCC patients. Conclusion. ZNF703 overexpression is associated with adverse prognosis in HNSCC, which might be a novel biomarker of HNSCC.

  10. A comparative proteomic analysis reveals important proteins for the fertilization and early embryonic development of the oyster Crassostrea gigas.

    Science.gov (United States)

    Huang, Xiaohong; Huan, Pin; Liu, Baozhong

    2017-01-01

    Molluscan development involves important features that are important to understanding not only molluscan ontogeny but also animal evolution. To gain insight into the gamete proteome and protein function in fertilization and early development, we analyzed the proteomes of unfertilized oocytes and early embryos (2/4-cell stage) of the Pacific oyster, Crassostrea gigas. An oocyte reference map containing 116 protein spots, of which 69 were identified, revealed a high abundance of vitellogenin-derived protein spots. The differentially regulated protein spots during fertilization were screened using comparative proteomic approaches. In total, 18 differentially regulated protein spots were screened, and 15 of these were identified and divided into three groups. The proteins belonging to the first group function in energy supply and antioxidation and are proposed to ensure successful fertilization by regulating the levels of adenosine triphosphate, resisting oxidative stress, and preventing polyspermy. The proteins of the second group are associated with protein synthesis and modification, reflecting active protein synthesis after fertilization. The three proteins belonging to the final group are hypothesized to function in the regulation of embryonic development through the establishment of cell polarity and modulation of methylation reactions in nuclei. These results will enhance our knowledge of molluscan fertilization and development. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Comparative study to develop a single method for retrieving wide class of recombinant proteins from classical inclusion bodies.

    Science.gov (United States)

    Padhiar, Arshad Ahmed; Chanda, Warren; Joseph, Thomson Patrick; Guo, Xuefang; Liu, Min; Sha, Li; Batool, Samana; Gao, Yifan; Zhang, Wei; Huang, Min; Zhong, Mintao

    2018-01-31

    The formation of inclusion bodies (IBs) is considered as an Achilles heel of heterologous protein expression in bacterial hosts. Wide array of techniques has been developed to recover biochemically challenging proteins from IBs. However, acquiring the active state even from the same protein family was found to be an independent of single established method. Here, we present a new strategy for the recovery of wide sub-classes of recombinant protein from harsh IBs. We found that numerous methods and their combinations for reducing IB formation and producing soluble proteins were not effective, if the inclusion bodies were harsh in nature. On the other hand, different practices with mild solubilization buffers were able to solubilize IBs completely, yet the recovery of active protein requires large screening of refolding buffers. With the integration of previously reported mild solubilization techniques, we proposed an improved method, which comprised low sarkosyl concentration, ranging from 0.05 to 0.1% coupled with slow freezing (- 1 °C/min) and fast thaw (room temperature), resulting in greater solubility and the integrity of solubilized protein. Dilution method was employed with single buffer to restore activity for every sub-class of recombinant protein. Results showed that the recovered protein's activity was significantly higher compared with traditional solubilization/refolding approach. Solubilization of IBs by the described method was proved milder in nature, which restored native-like conformation of proteins within IBs.

  12. Comparative proteomic analysis of Streptococcus suis biofilms and planktonic cells that identified biofilm infection-related immunogenic proteins.

    Science.gov (United States)

    Wang, Yang; Yi, Li; Wu, Zongfu; Shao, Jing; Liu, Guangjin; Fan, Hongjie; Zhang, Wei; Lu, Chengping

    2012-01-01

    Streptococcus suis (SS) is a zoonotic pathogen that causes severe disease symptoms in pigs and humans. Biofilms of SS bind to extracellular matrix proteins in both endothelial and epithelial cells and cause persistent infections. In this study, the differences in the protein expression profiles of SS grown either as planktonic cells or biofilms were identified using comparative proteomic analysis. The results revealed the existence of 13 proteins of varying amounts, among which six were upregulated and seven were downregulated in the Streptococcus biofilm compared with the planktonic controls. The convalescent serum from mini-pig, challenged with SS, was applied in a Western blot assay to visualize all proteins from the biofilm that were grown in vitro and separated by two-dimensional gel electrophoresis. A total of 10 immunoreactive protein spots corresponding to nine unique proteins were identified by MALDI-TOF/TOF-MS. Of these nine proteins, five (Manganese-dependent superoxide dismutase, UDP-N-acetylglucosamine 1-carboxyvinyltransferase, ornithine carbamoyltransferase, phosphoglycerate kinase, Hypothetical protein SSU05_0403) had no previously reported immunogenic properties in SS to our knowledge. The remaining four immunogenic proteins (glyceraldehyde-3-phosphate dehydrogenase, hemolysin, pyruvate dehydrogenase and DnaK) were identified under both planktonic and biofilm growth conditions. In conclusion, the protein expression pattern of SS, grown as biofilm, was different from the SS grown as planktonic cells. These five immunogenic proteins that were specific to SS biofilm cells may potentially be targeted as vaccine candidates to protect against SS biofilm infections. The four proteins common to both biofilm and planktonic cells can be targeted as vaccine candidates to protect against both biofilm and acute infections.

  13. Incidence and 5-year survival rate for head and neck cancers in Grenada compared to the African American population over the period 1991-2010.

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    du Plessis, Maira; Hage, Robert

    2017-11-01

    Very little data exist on the incidence and burden of cancer in the individual Caribbean countries. Some data are available for larger areas, reported under a bigger geographical region; Latin America and the Caribbean, but many of the individual countries are not included. One of the main reasons is a lack of official cancer registries. Data are usually collected from hospital records or private physician records, and since it is not in an official registry, these data are not always accessible for inclusion in databases such as SEER and GLOBOCAN. Grenada is one of the countries that currently does not have a registry. Our aim is to report on the incidence for head and neck cancer with subcategories; hypopharynx, oropharynx, oral cavity, salivary glands, and larynx from data collected by the sole ear nose and throat specialist over a 20-year period. The age adjusted incidence per 100,000 for these cancers, whether combined or individually, is lower than that of similar populations. The incidence in males is only slightly higher than those reported in some parts of Africa. In females, only Eastern Africa is reported to have a lower incidence than that found in our study. While the incidence of oral cancers is lower than that of African Americans, the survival rate is comparable. Socioeconomic status, lack of infrastructure, and advanced stage at diagnosis appear to be closely related to the survival rate. Incidence reports suggest that incidence of head and neck cancers in individuals of African descent is lower than other populations. It is therefore not surprising that the incidence in Grenada is relatively low, although the incidence may be underestimated.

  14. The character of haemostatic disorders and level of protein S-100 in acute ischaemic stroke can affect survival in the first week of follow-up: a pilot study.

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    Jastrzębska, Maria; Chełstowski, Kornel; Siennicka, Aldona; Grzelec, Halina; Bajer-Czajkowska, Anna; Rybicka, Marta; Clark, Jeremy; Nowacki, Przemysław

    2011-07-01

    Disorders of haemostasis which result in ischaemic stroke usually appear as thromboembolism in peripheral veins and the pulmonary circulation, and to a lesser extent as coagulopathy. The S-100 protein, a marker of stroke, correlates positively with the neurological deficit National Institutes of Health Stroke Scale (NIHSS). We adopted the hypothesis that early death of patients with acute ischaemic stroke can be explained by changes in blood coagulation and fibrinolysis. The study included 84 patients hospitalized with acute ischaemic stroke. Three groups were created: I (death between 1 and 2 days), II (death between 5 and 7 days) and III (with no deaths in hospital). We measured levels of fibrinogen, antithrombin, D-dimers, plasmin-antiplasmin complexes, plasminogen and clotting times (prothrombin time and activated partial thromboplastin time), platelet number, euglobulin clot lysis time (ECLTindex) and S-100 protein, C-reactive protein and white blood cells (WBCs). Group I had lower concentrations of fibrinogen compared to groups II (3.13 vs. 4.18, P<0.01) and III (3.13 vs. 3.77, P<0.02) and higher levels of D-dimers (3643 vs. 2278, P<0.05), higher concentrations of plasmin-antiplasmin complexes (1410 vs. 882, P=0.03) and a lower ECLTindex (152 vs. 219, P<0.02) when compared with group III. Group I also had higher concentrations of protein S-100 (2.09 vs. 0.61, P<0.001), higher NIHSS (18.0 vs. 13.2, P=0.073) and number of WBC (14.1 vs. 11.1, P<0.02) than in group III. The observed abnormalities in haemostasis, either found systemically or locally as cerebral microvascular thrombosis, may be factors potentially associated with death of patients with the shortest survival time.

  15. Cascading effects from survival to physiological activities, and gene expression of heat shock protein 90 on the abalone Haliotis discus hannai responding to continuous thermal stress.

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    Park, Kiyun; Lee, Jung Sick; Kang, Ju-Chan; Kim, Jae Won; Kwak, Ihn-Sil

    2015-02-01

    Increasing temperatures can be a significant stressor for aquatic organisms. Abalones, a type of large marine gastropods, are the most commercially important species in aquaculture for Asia. To evaluate the potential ecological risk posed by temperature stress, we measured biological responses such as survival rate, adhesion ability (falling rate), and foot abnormalities in the abalone Haliotis discus hannai. Additionally, biochemical and molecular responses were evaluated in H. discus hannai exposed to various temperature gradients. The survival rate was reduced in abalones exposed to relative high temperatures (more than 26 °C). Increased temperature stress induced a higher falling rate and abnormal foot structure. Furthermore, increased antioxidant enzyme activities were observed in abalones exposed to relative high temperatures (26 and 28 °C). The activities of superoxide dismutase were induced in a time-dependent manner after high temperature stress. Generally, heat shock protein 90 also increased significantly in H. discus hannai exposed to temperature gradients (more than 24 °C) for 12 h. These results provide valuable information regarding stress responses to increased temperatures, in H. discus hannai: adverse biological and molecular outcomes could be utilized as risk assessments and stress monitoring of marine ecosystems under increased water temperatures. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. An inherited variant in the gene coding for vitamin D-binding protein and survival from cutaneous melanoma: a BioGenoMEL study

    Science.gov (United States)

    Davies, John R; Field, Sinead; Randerson-Moor, Juliette; Harland, Mark; Kumar, Rajiv; Anic, Gabriella M; Nagore, Eduardo; Hansson, Johan; Höiom, Veronica; Jönsson, Göran; Gruis, Nelleke A; Park, Jong Y; Guan, Jian; Sivaramakrishna Rachakonda, P; Wendt, Judith; Pjanova, Dace; Puig, Susana; Schadendorf, Dirk; Okamoto, Ichiro; Olsson, Håkan; Affleck, Paul; García-Casado, Zaida; Puig-Butille, Joan Anton; Stratigos, Alexander J; Kodela, Elizabeth; Donina, Simona; Sucker, Antje; Hosen, Ismail; Egan, Kathleen M; Barrett, Jennifer H; van Doorn, Remco; Bishop, D Timothy; Newton-Bishop, Julia

    2014-01-01

    An association between low serum vitamin D levels and poorer melanoma survival has been reported. We have studied inheritance of a polymorphism of the GC gene, rs2282679, coding for the vitamin D-binding protein, which is associated with lower serum levels of vitamin D, in a meta-analysis of 3137 melanoma patients. The aim was to investigate evidence for a causal relationship between vitamin D and outcome (Mendelian randomization). The variant was not associated with reduced overall survival (OS) in the UK cohort, per-allele hazard ratio (HR) for death 1.23 (95% confidence interval (CI) 0.93, 1.64). In the smaller cohorts, HR in OS analysis was 1.07 (95% CI 0.88, 1.3) and for all cohorts combined, HR for OS was 1.09 (95% CI 0.93, 1.29). There was evidence of increased melanoma-specific deaths in the seven cohorts for which these data were available. The lack of unequivocal findings despite the large sample size illustrates the difficulties of implementing Mendelian randomization. PMID:24219834

  17. Multiple arterial grafting confers survival advantage compared to percutaneous intervention with drug-eluting stents in multivessel coronary artery disease: A propensity score adjusted analysis.

    Science.gov (United States)

    Raja, Shahzad G; Benedetto, Umberto; Ilsley, Charles D; Amrani, Mohamed

    2015-01-01

    The best revascularisation strategy for multivessel coronary artery disease (MVD) is still controversial. Percutaneous coronary intervention (PCI) utilising drug eluting stents (DES) has emerged as an acceptable alternative to conventional coronary artery bypass grafting (CABG) in the last decade. However, multiple arterial grafting (MAG) is superior revascularisation strategy compared with conventional CABG utilising single internal mammary artery and currently there is a paucity of comparison of DES and MAG. We aimed to investigate whether MAG offers advantage over DES-PCI in MVD. A total of 6126 patients with MVD (≥ 2 vessel) underwent CABG (n = 4652) or PCI (n = 1474) at a single institution. MAG was performed in 1372 CABG cases and DES were implanted in 1222 PCI cases. Propensity score adjusted analysis was performed to investigate the potential survival advantage of MAG over PCI. Mean follow-up was 4.9 years. Risk for late death was comparable after DES-PCI and conventional CABG (HR 1.11; 95%CI 0.9 to 1.33; P = 0.25). However, DES-PCI was associated with an increased risk for late death compared to MAG (HR 1.53; 95%CI 1.08 to 2.91; P = 0.02). DES-PCI was also associated with a 3.51 fold increased risk for repeat revascularisation over MAG (95%CI 2.60 to 4.75; P compared to DES-PCI. When feasible, MAG should be strongly recommended in patients with MVD. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  18. Intradermal vaccination with hollow microneedles: A comparative study of various protein antigen and adjuvant encapsulated nanoparticles.

    Science.gov (United States)

    Du, Guangsheng; Hathout, Rania M; Nasr, Maha; Nejadnik, M Reza; Tu, Jing; Koning, Roman I; Koster, Abraham J; Slütter, Bram; Kros, Alexander; Jiskoot, Wim; Bouwstra, Joke A; Mönkäre, Juha

    2017-09-21

    In this study, we investigated the potential of intradermal delivery of nanoparticulate vaccines to modulate the immune response of protein antigen using hollow microneedles. Four types of nanoparticles covering a broad range of physiochemical parameters, namely poly (lactic-co-glycolic) (PLGA) nanoparticles, liposomes, mesoporous silica nanoparticles (MSNs) and gelatin nanoparticles (GNPs) were compared. The developed nanoparticles were loaded with a model antigen (ovalbumin (OVA)) with and without an adjuvant (poly(I:C)), followed by the characterization of size, zeta potential, morphology, and loading and release of antigen and adjuvant. An in-house developed hollow-microneedle applicator was used to inject nanoparticle suspensions precisely into murine skin at a depth of about 120μm. OVA/poly(I:C)-loaded nanoparticles and OVA/poly(I:C) solution elicited similarly strong total IgG and IgG1 responses. However, the co-encapsulation of OVA and poly(I:C) in nanoparticles significantly increased the IgG2a response compared to OVA/poly(I:C) solution. PLGA nanoparticles and liposomes induced stronger IgG2a responses than MSNs and GNPs, correlating with sustained release of the antigen and adjuvant and a smaller nanoparticle size. When examining cellular responses, the highest CD8(+) and CD4(+) T cell responses were induced by OVA/poly(I:C)-loaded liposomes. In conclusion, the applicator controlled hollow microneedle delivery is an excellent method for intradermal injection of nanoparticle vaccines, allowing selection of optimal nanoparticle formulations for humoral and cellular immune responses. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  19. B-cell receptor-associated protein 31 regulates human embryonic stem cell adhesion, stemness, and survival via control of epithelial cell adhesion molecule.

    Science.gov (United States)

    Kim, Won-Tae; Seo Choi, Hong; Min Lee, Hyun; Jang, Young-Joo; Ryu, Chun Jeih

    2014-10-01

    B-Cell receptor-associated protein 31 (BAP31) regulates the export of secreted membrane proteins from the endoplasmic reticulum (ER) to the downstream secretory pathway. Previously, we generated a monoclonal antibody 297-D4 against the surface molecule on undifferentiated human embryonic stem cells (hESCs). Here, we found that 297-D4 antigen was localized to pluripotent hESCs and downregulated during early differentiation of hESCs and identified that the antigen target of 297-D4 was BAP31 on the hESC-surface. To investigate the functional role of BAP31 in hESCs, BAP31 expression was knocked down by small interfering RNA. BAP31 depletion impaired hESC self-renewal and pluripotency and drove hESC differentiation into multicell lineages. BAP31 depletion hindered hESC proliferation by arresting cell cycle at G0/G1 phase and inducing caspase-independent cell death. Interestingly, BAP31 depletion reduced hESC adhesion to extracellular matrix (ECM). Analysis of cell surface molecules showed decreased expression of epithelial cell adhesion molecule (EpCAM) in BAP31-depleted hESCs, while ectopic expression of BAP31 elevated the expression of EpCAM. EpCAM depletion also reduced hESC adhesion to ECM, arrested cell cycle at G0/G1 phase and induced cell death, producing similar effects to those of BAP31 depletion. BAP31 and EpCAM were physically associated and colocalized at the ER and cell surface. Both BAP31 and EpCAM depletion decreased cyclin D1 and E expression and suppressed PI3K/Akt signaling, suggesting that BAP31 regulates hESC stemness and survival via control of EpCAM expression. These findings provide, for the first time, mechanistic insights into how BAP31 regulates hESC stemness and survival via control of EpCAM expression. © 2014 AlphaMed Press.

  20. Optimization of Ziziphora clinopodiodes essential oil microencapsulation by whey protein isolate and pectin: A comparative study.

    Science.gov (United States)

    Hosseinnia, Mahmoud; Khaledabad, Mohammad Alizadeh; Almasi, Hadi

    2017-08-01

    The performance of whey protein isolate (WPI) and pectin as wall materials in encapsulation of Ziziphora clinopodiodes essential oil by ultrasonication method was compared. In this regard, using the response surface methodology, the influence of ultrasonication (US) power (50-150W) and core-coating ratio (10-100%) on the properties of microcapsules was evaluated. Increasing US power and core-coating ratio, caused to increase and decrease the particle size, respectively. The polydispersity index (PDI) of WPI coated microcapsules was increased by increasing of US power. The Zeta potential values were increased by increasing of core-coating ratio. Also, the effect of core-coating ratio on encapsulation efficiency was more than US power. Morphological studies by SEM on optimized microcapsules showed regular spherical shapes. X-ray diffraction analysis revealed that the type of the wall material had no effect on the structural properties of the microparticles. FT-IR analysis confirmed the pronounced effect of electrostatic interactions in the formation of microcapsules. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Nrf1 CNC-bZIP protein promotes cell survival and nucleotide excision repair through maintaining glutathione homeostasis.

    Science.gov (United States)

    Han, Weinong; Ming, Mei; Zhao, Rui; Pi, Jingbo; Wu, Chunli; He, Yu-Ying

    2012-05-25

    Skin cancer is the most common cancer in the United States. Its major environmental risk factor is UVB radiation in sunlight. In response to UVB damage, epidermal keratinocytes activate a specific repair pathway, i.e. nucleotide excision repair, to remove UVB-induced DNA lesions. However, the regulation of UVB response is not fully understood. Here we show that the long isoform of the nuclear factor erythroid 2-related factor 1 (Nrf1, also called NFE2L1), a cytoprotective transcription factor critical for the expression of multiple antioxidant response element-dependent genes, plays an important role in the response of keratinocytes to UVB. Nrf1 loss sensitized keratinocytes to UVB-induced apoptosis by up-regulating the expression of the proapoptotic Bcl-2 family member Bik through reducing glutathione levels. Knocking down Bik reduced UVB-induced apoptosis in Nrf1-inhibited cells. In UVB-irradiated surviving cells, however, disruption of Nrf1 impaired nucleotide excision repair through suppressing the transcription of xeroderma pigmentosum C (XPC), a factor essential for initiating the global genome nucleotide excision repair by recognizing the DNA lesion and recruiting downstream factors. Nrf1 enhanced XPC expression by increasing glutathione availability but was independent of the transcription repressor of XPC. Adding XPC or glutathione restored the DNA repair capacity in Nrf1-inhibited cells. Finally, we demonstrate that Nrf1 levels are significantly reduced by UVB radiation in mouse skin and are lower in human skin tumors than in normal skin. These results indicate a novel role of Nrf1 in UVB-induced DNA damage repair and suggest Nrf1 as a tumor suppressor in the skin.

  2. Soy Protein Compared with Milk Protein in a Western Diet Increases Gut Microbial Diversity and Reduces Serum Lipids in Golden Syrian Hamsters.

    Science.gov (United States)

    Butteiger, Dustie N; Hibberd, Ashley A; McGraw, Nancy J; Napawan, Nida; Hall-Porter, Janine M; Krul, Elaine S

    2016-04-01

    Diet is a major factor influencing the composition and metabolic activity of the gut microbiota. This study investigated the effect of soy compared with dairy protein on the gut microbiota of hamsters to determine whether changes in microbiota could account for soy protein's lipid lowering properties. Thirty-two 6- to 8-wk-old, male Golden Syrian hamsters were fed a Western diet containing 22% (%wt) milk protein isolate (MPI) as the single protein source for 3 wk followed by 6 wk of one of 4 diets containing either [22% protein (%wt)]: MPI, soy protein concentrate (SPC), partially hydrolyzed soy protein isolate (SPI1), or intact soy protein isolate. Serum lipids, hepatic gene expression, and gut microbial populations were evaluated. Serum total and LDL-cholesterol concentrations were lower in the SPC-fed group (183 ± 9.0 and 50 ± 4.2 mg/dL, respectively) than in the MPI group (238 ± 8.7 and 72 ± 3.9 mg/dL, respectively) (Psoy-fed groups than in the MPI-fed group (Psoy-fed group than in the MPI-fed group (Psoy protein was associated with higher expression of 3-hydroxy-3-methylglutaryl-CoA reductase (Hmgcr), lanosterol synthase (Lss), and farnesyl-diphosphosphate farnesyl-transferase 1 (Fdft1) (1.6-2.5-fold higher), and lower steroyl-CoA desaturase-1 (Scd1) expression (37-46% lower) in all soy-fed groups (Psoy protein may reduce lipogenesis through alterations of the gut microbial community. © 2016 American Society for Nutrition.

  3. Compared with radical nephrectomy, nephron-sparing surgery offers a long-term survival advantage in patients between the ages of 20 and 44 years with renal cell carcinomas (≤4 cm): an analysis of the SEER database.

    Science.gov (United States)

    Daugherty, Michael; Bratslavsky, Gennady

    2014-07-01

    Compared with radical nephrectomy (RN), partial nephrectomy (PN) decreases the risk of developing chronic kidney disease. Although numerous studies have demonstrated the survival advantage of PN in older patients, they have been criticized by selection bias toward the procedure owing to comorbidities. We hypothesized that long-standing effects of renal preservation would manifest in a survival advantage of a younger patient population, where selection bias owing to comorbidities is minimized. The Surveillance, Epidemiology, and End Results 18-registries database was queried for patients aged 20 to 44 years surgically treated between 1993 and 2003 for renal cell carcinoma (RCC) ≤ 4 cm with known grade and histology. Patients with prior RCC, multiple tumors, and metastatic or locally advanced disease were excluded. The final cohorts consisted of 222 and 494 subjects treated with PN and RN, respectively. The chi-square and log-rank analyses compared patient and tumor characteristics and patient survival, respectively. There were no differences between the groups in demographics or tumor characteristics. Additionally, there was no difference in cancer-specific survival at 5 or 10 years (P = 0.34 and P = 0.1, respectively). Although there was no difference in 5-year overall survival (P = 0.07), PN offered an advantage in 10-year overall survival (P = 0.025). Present Surveillance, Epidemiology, and End Results analyses demonstrate that compared with RN, PN improved overall survival in patients with small, localized RCC. As expected, the survival advantage is observed late and supports the importance of long-term renal functional preservation. Although our study is limited by lack of comorbidities, the results suggest that detrimental effects of RN may have implications on overall survival in younger patients with RCC. © 2013 Published by Elsevier Inc.

  4. Systematic functional comparative analysis of four single-stranded DNA-binding proteins and their affection on viral RNA metabolism.

    Directory of Open Access Journals (Sweden)

    Haiyan Shi

    Full Text Available The accumulation of single-stranded DNA-binding (SSB proteins is essential for organisms and has various applications. However, no study has simultaneously and systematically compared the characteristics of SSB proteins. In addition, SSB proteins may bind RNA and play an unknown biological role in RNA metabolism. Here, we expressed a novel species of SSB protein derived from Thermococcus kodakarensis KOD1 (KOD, as well as SSB proteins from Thermus thermophilus (TTH, Escherichia coli, and Sulfolobus Solfataricus P2 (SSOB, abbreviated kod, tth, bl21, and ssob, respectively. These SSB proteins could bind ssDNA and viral RNA. bl21 resisted heat treatment for more than 9 h, Ssob and kod could withstand 95°C for 10 h and retain its ssDNA- and RNA-binding ability. Four SSB proteins promoted the specificity of the DNA polymerase in PCR-based 5- and 9-kb genome fragment amplification. kod also increased the amplification of a 13-kb PCR product, and SSB protein-bound RNA resisted Benzonase digestion. The SSB proteins could also enter the host cell bound to RNA, which resulted in modulation of viral RNA metabolism, particularly ssob and bl21.

  5. COMPARATIVE STUDY ON ANGIOTENSIN CONVERTING ENZYME INHIBITORY ACTIVITY OF HYDROLYSATE OF MEAT PROTEIN OF INDONESIAN LOCAL LIVESTOCKS

    Directory of Open Access Journals (Sweden)

    J. Jamhari

    2014-10-01

    Full Text Available The experiment was conducted to investigate the angiotensin converting enzyme (ACE inhibitoryactivity of hydrolysate in meat protein of Bali cattle, Kacang goat, native chicken, and local duck. Themeats of Bali cattle, Kacang goat, native chicken, and local duck were used in this study. The meatswere ground using food processor added with aquadest to obtain meat extract. The meat extracts werethen hydrolyzed using protease enzymes to obtain hydrolysate of meat protein. Protein concentration ofmeat extract and hydrolysate of meat protein were determined, and were confirmed by sodium dodecylsulfate - poly acrylamide gel electrophoresis (SDS-PAGE. ACE inhibitory activity of hydrolysate ofmeat protein derived from Bali cattle, Kacang goat, native chicken, and local duck was also determined.The results showed that protein concentration of hydrolysate of meat protein of Bali cattle, Kacang goat,native chicken, and local duck meat was significantly higher than their meat extracts. SDS-PAGEanalysis indicated that hydrolysate of meat protein of Bali cattle, Kacang goat, native chicken, and localduck had more peptides with lower molecular weight, compared to their meat extracts. Hydrolysate ofmeat protein of Bali cattle, Kacang goat, native chicken, and local duck had potencies in inhibiting ACEactivity, so it will potentially reduce blood pressure.

  6. Optimizing Protein Intake in Adults: Interpretation and Application of the Recommended Dietary Allowance Compared with the Acceptable Macronutrient Distribution Range.

    Science.gov (United States)

    Wolfe, Robert R; Cifelli, Amy M; Kostas, Georgia; Kim, Il-Young

    2017-03-01

    The adult RDA is defined as the average daily level of intake sufficient to meet the nutrient requirements of nearly all healthy people. The RDA for protein for adults ≥18 y of age (0.8 g/kg) has been essentially unchanged for >70 y. In practice, the RDA for protein was derived to estimate the minimum amount of protein that must be eaten to avoid a loss of body nitrogen. The Acceptable Macronutrient Distribution Range (AMDR) (10-35% of calories as protein) was developed to express dietary recommendations in the context of a complete diet. It is noteworthy that the lowest level of protein intake reflected in the AMDR is higher than that of the RDA. Furthermore, recent studies, particularly in older individuals, suggest specific health benefits at levels of protein intake that significantly exceed the RDA. Translation of protein intake recommendations for the general adult population into dietary guidance for individuals requires an understanding of the derivation and intended use of both the protein RDA and AMDR. The following discussion will describe limitations to the derivation and practical application of the RDA compared with the use of the AMDR to help maximize health benefits associated with higher protein intake by using flexible calories inherent in different dietary patterns. © 2017 American Society for Nutrition.

  7. Comparative Evaluation of Recombinant Protein Production in Different Biofactories: The Green Perspective

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    Matilde Merlin

    2014-01-01

    Full Text Available In recent years, the production of recombinant pharmaceutical proteins in heterologous systems has increased significantly. Most applications involve complex proteins and glycoproteins that are difficult to produce, thus promoting the development and improvement of a wide range of production platforms. No individual system is optimal for the production of all recombinant proteins, so the diversity of platforms based on plants offers a significant advantage. Here, we discuss the production of four recombinant pharmaceutical proteins using different platforms, highlighting from these examples the unique advantages of plant-based systems over traditional fermenter-based expression platforms.

  8. Retinoblastoma protein expression is an independent predictor of both radiation response and survival in muscle invasive bladder cancer

    DEFF Research Database (Denmark)

    Agerbæk, Mads; Alsner, Jan; Marcussen, Niels

    2003-01-01

    The objective of the study was to investigate the predictive value of various clinical, biochemical, and histopathological parameters, with special emphasis on the expression of the retinoblastoma protein (pRB), on the radiation response in bladder cancer. In order to obtain a truly objective....... Expression of pRB was assessed by immunohistochemical staining as present or absent. Complete response to radiotherapy was obtained in 42 of 106 evaluable patients (40%). Predictive for CR to radiotherapy, in univariate analysis, was transurethral resection (as opposed to biopsy), B-haemoglobin, no upper...... urinary retention, and loss of pRB staining. Loss of pRB staining was the strongest independent predictor of radiation response in multivariate logistic regression analysis and absence of upper urinary retention was the only other significant factor. Loss of pRB was the only parameter showing...

  9. Comparative proteomics reveals a role for seed storage protein AmA1 in cellular growth, development, and nutrient accumulation.

    Science.gov (United States)

    Agrawal, Lalit; Narula, Kanika; Basu, Swaraj; Shekhar, Shubhendu; Ghosh, Sudip; Datta, Asis; Chakraborty, Niranjan; Chakraborty, Subhra

    2013-11-01

    Seed storage proteins are known to be utilized as carbon and nitrogen source for growing seedlings and thus are considered as potential candidates for nutritional improvement. However, their precise function remains unknown. We have earlier shown that ectopic expression of a seed storage protein, AmA1, leads to increase in protein besides high tuber yield in potato. To elucidate the AmA1-regulated molecular mechanism affecting increased protein synthesis, reserve accumulation, and enhanced growth, a comparative proteomics approach has been applied to tuber life-cycle between wild-type and AmA1 potato. The differential display of proteomes revealed 150 AmA1-responsive protein spots (ARPs) that change their intensities more than 2.5-fold. The LC-ESI-MS/MS analyses led to the identification of 80 ARPs presumably associated with cell differentiation, regulating diverse functions, viz., protein biogenesis and storage, bioenergy and metabolism, and cell signaling. Metabolome study indicated up-regulation of amino acids paralleling the proteomics analysis. To validate this, we focused our attention on anatomical study that showed differences in cell size in the cortex, premedullary zone and pith of the tuber, coinciding with AmA1 expression and localization. Further, we interrogated the proteome data using one-way analysis of variance, cluster, and partial correlation analysis that identified two significant protein modules and six small correlation groups centered around isoforms of cysteine protease inhibitor, actin, heat shock cognate protein 83 and 14-3-3, pointing toward AmA1-regulated overlapping processes of protein enhancement and cell growth perhaps through a common mechanism of function. A model network was constructed using the protein data sets, which aim to show how target proteins might work in coordinated fashion and attribute to increased protein synthesis and storage reserve accumulation in AmA1 tubers on one hand and organ development on the other.

  10. Comparative proteome analysis of Saccharomyces cerevisiae: A global overview of in vivo targets of the yeast activator protein 1

    Directory of Open Access Journals (Sweden)

    Jun He

    2012-06-01

    Full Text Available Abstract Background The activity of the yeast activator protein 1 (Yap1p increases under stress conditions, which leads to enhanced transcription of a number of genes encoding protective enzymes or other proteins. To obtain a global overview of changes in expression of Yap1p-targeted proteins, we compared a Yap1p-overexpressing transformant with a control transformant by triplicate analysis of the proteome using two-dimensional gel electrophoresis (2-DE. Proteins of interest were identified using MALDI-MS or LC-MS/MS. Results The relative quantities of 55 proteins were elevated significantly upon overexpression of Yap1p, and most of these proteins were found to have a Yap1p-binding site upstream of their coding sequences. Interestingly, the main metabolic enzymes in the glycolysis and pyruvate-ethanol pathways showed a significant increase in the Yap1p-overexpressing transformant. Moreover, a comparison of our proteome data with transcriptome data from the literature suggested which proteins were regulated at the level of the proteome, and which proteins were regulated at the level of the transcriptome. Eight proteins involved in stress response, including seven heat-shock and chaperone proteins, were significantly more abundant in the Yap1p-overexpressing transformant. Conclusions We have investigated the general protein composition in Yap1p-overexpressing S. cerevisiae using proteomic techniques, and quantified the changes in the expression of the potential Yap1p-targeted proteins. Identification of the potential Yap1p targets and analysis of their role in cellular processes not only give a global overview of the ubiquitous cellular changes elicited by Yap1p, but also provide the framework for understanding the mechanisms behind Yap1p-regulated stress response in yeast.

  11. Comparative proteome analysis of Saccharomyces cerevisiae: a global overview of in vivo targets of the yeast activator protein 1.

    Science.gov (United States)

    Jun, He; Kieselbach, Thomas; Jönsson, Leif J

    2012-06-09

    The activity of the yeast activator protein 1 (Yap1p) increases under stress conditions, which leads to enhanced transcription of a number of genes encoding protective enzymes or other proteins. To obtain a global overview of changes in expression of Yap1p-targeted proteins, we compared a Yap1p-overexpressing transformant with a control transformant by triplicate analysis of the proteome using two-dimensional gel electrophoresis (2-DE). Proteins of interest were identified using MALDI-MS or LC-MS/MS. The relative quantities of 55 proteins were elevated significantly upon overexpression of Yap1p, and most of these proteins were found to have a Yap1p-binding site upstream of their coding sequences. Interestingly, the main metabolic enzymes in the glycolysis and pyruvate-ethanol pathways showed a significant increase in the Yap1p-overexpressing transformant. Moreover, a comparison of our proteome data with transcriptome data from the literature suggested which proteins were regulated at the level of the proteome, and which proteins were regulated at the level of the transcriptome. Eight proteins involved in stress response, including seven heat-shock and chaperone proteins, were significantly more abundant in the Yap1p-overexpressing transformant. We have investigated the general protein composition in Yap1p-overexpressing S. cerevisiae using proteomic techniques, and quantified the changes in the expression of the potential Yap1p-targeted proteins. Identification of the potential Yap1p targets and analysis of their role in cellular processes not only give a global overview of the ubiquitous cellular changes elicited by Yap1p, but also provide the framework for understanding the mechanisms behind Yap1p-regulated stress response in yeast.

  12. Effect of stocking density and source of animal protein on growth and survival of rainbow trout fingerlings in flow-through system at Nuwakot, Nepal

    Directory of Open Access Journals (Sweden)

    Prem Timalsina

    2017-11-01

    Full Text Available An experiment was conducted in outdoor nursing raceways with flow-through system (2.7 m2 at the Fisheries Research Station, Trishuli, Nuwakot Nepal for 249 days to evaluate the effect of stocking density and sources of animal protein on growth and survival of rainbow trout fingerlings production. The experiment was conducted in 2 × 2 factorial completely randomized design having two stocking densities, (density-1: 10 kg/m2 and density-2: 12.5 kg/m2 and two diets (diet-1: shrimp meal based diet and diet-2: 5% bovine blood meal mixed diet. All treatments were replicated thrice. Water from the Trishuli river was used and 50 cm water depth was maintained in all treatments. Initial feeding rate of 10% of the body weight was gradually reduced to 8, 7, 6, 5, 4 and 3% was maintained for the subsequent months. Feeding was done 5 times a day throughout the study period. Results showed that the mean total harvest weight in diet-1 (30.17 ± 1.34 kg was significantly higher than in diet-2 (22.77 ± 1.34 kg; however, no significance difference was observed at stocking density levels. Mean survival of fish in diet-1 (60.30 ± 2.08% was significantly higher than diet-2 (47.78 ± 2.08%. Similarly, survivability of fish in density-1 (63.45 ± 2.08% was significantly higher than in density-2 (44.63 ± 2.08%. The mean dissolve oxygen at density-2 (8.89 ± 0.02 mg/L was significantly lower to that of density-1 (8.94 ± 0.02 mg/L and B:C ratio was high with shrimp meal based diet and high stocking density (T3. In the present study, the treatment with shrimp meal based diet and high stocking density (T3 was superior with high mean total harvest weight, gross fish yield, low FCR and high B: C ratio than other treatment combinations. The present study demonstrated that growth, production and survival performances of rainbow trout in the present experimental condition were not satisfactory by substituting a part of shrimp meal by blood meal.

  13. Is it possible to compare PSA recurrence-free survival after surgery and radiotherapy using revised ASTRO criterion--"nadir + 2"?

    Science.gov (United States)

    Nielsen, Matthew E; Makarov, Danil V; Humphreys, Elizabeth; Mangold, Leslie; Partin, Alan W; Walsh, Patrick C

    2008-08-01

    The new American Society for Therapeutic Radiology and Oncology/Radiation Therapy Oncology Group consensus definition of biochemical failure after radiotherapy for prostate cancer is defined as a prostate-specific antigen level at or greater than the absolute nadir PSA level plus 2 ng/mL. Because this definition inevitably will be used to compare cancer control rates after radiotherapy to those after surgery, this study examined the effect of this comparison. We reviewed the data from 2570 men who had undergone radical prostatectomy from 1985 to 2004. Biochemical failure was defined as any measurable PSA level of 0.2 ng/mL or greater. We evaluated how the nadir+2 definition affected the failure rate when applied to this series. The actuarial 5, 10, and 15-year biochemical recurrence-free survival probability with failure defined as a PSA level of 0.2 ng/mL or more and a PSA level of 2 ng/mL or more was 88.6%, 81.2%, and 78.1% and 94.6%, 89.4%, and 84.3%, respectively (P <0.0001). The median time to biochemical progression was 2.8 years for the greater than 0.2 ng/mL definition and 7.9 years for the 2 ng/mL or more definition. The nadir+2 definition systematically overestimated the biochemical recurrence-free survival, even after stratifying patients into standard prognostic risk groups, especially in men who developed local recurrence. When applied to a mature series of surgically treated patients with localized prostate cancer, the American Society for Therapeutic Radiology and Oncology "nadir+2" definition resulted in a systematic delay in the determination of biochemical failure. Because patients in this series who experienced a detectable PSA level took more than 5 years to progress to a PSA level of 2 ng/mL or greater, the 5-year biochemical control rates with the definition of 0.2 ng/mL or more should be compared with the 10-year biochemical control rates using the nadir+2 definition.

  14. Protein A-mouse acidic mammalian chitinase-V5-His expressed in periplasmic space of Escherichia coli possesses chitinase functions comparable to CHO-expressed protein.

    Directory of Open Access Journals (Sweden)

    Akinori Kashimura

    Full Text Available Acidic mammalian chitinase (AMCase has been shown to be associated with asthma in mouse models, allergic inflammation and food processing. Here, we describe an E. coli-expression system that allows for the periplasmic production of active AMCase fused to Protein A at the N-terminus and V5 epitope and (His6 tag (V5-His at the C-terminus (Protein A-AMCase-V5-His in E. coli. The mouse AMCase cDNA was cloned into the vector pEZZ18, which is an expression vector containing the Staphylococcus Protein A promoter, with the signal sequence and truncated form of Protein A for extracellular expression in E. coli. Most of the Protein A-AMCase-V5-His was present in the periplasmic space with chitinolytic activity, which was measured using a chromogenic substrate, 4-nitrophenyl N,N'-diacetyl-β-D-chitobioside. The Protein A-AMCase-V5-His was purified from periplasmic fractions using an IgG Sepharose column followed by a Ni Sepharose chromatography. The recombinant protein showed a robust peak of activity with a maximum observed activity at pH 2.0, where an optimal temperature was 54°C. When this protein was preincubated between pH 1.0 and pH 11.0 on ice for 1 h, full chitinolytic activity was retained. This protein was also heat-stable till 54°C, both at pH 2.0 and 7.0. The chitinolytic activity of the recombinant AMCase against 4-nitrophenyl N,N'-diacetyl-β-D-chitobioside was comparable to the CHO-expressed AMCase. Furthermore, the recombinant AMCase bound to chitin beads, cleaved colloidal chitin and released mainly N,N'-diacetylchitobiose fragments. Thus, the E. coli-expressed Protein A-mouse AMCase-V5-His fusion protein possesses chitinase functions comparable to the CHO-expressed AMCase. This recombinant protein can be used to elucidate detailed biomedical functions of the mouse AMCase.

  15. Protein A-Mouse Acidic Mammalian Chitinase-V5-His Expressed in Periplasmic Space of Escherichia coli Possesses Chitinase Functions Comparable to CHO-Expressed Protein

    Science.gov (United States)

    Kida, Yuta; Iwabuchi, Kokoro; Matsushima, Yudai; Sakaguchi, Masayoshi; Sugahara, Yasusato; Oyama, Fumitaka

    2013-01-01

    Acidic mammalian chitinase (AMCase) has been shown to be associated with asthma in mouse models, allergic inflammation and food processing. Here, we describe an E. coli-expression system that allows for the periplasmic production of active AMCase fused to Protein A at the N-terminus and V5 epitope and (His)6 tag (V5-His) at the C-terminus (Protein A-AMCase-V5-His) in E. coli. The mouse AMCase cDNA was cloned into the vector pEZZ18, which is an expression vector containing the Staphylococcus Protein A promoter, with the signal sequence and truncated form of Protein A for extracellular expression in E. coli. Most of the Protein A-AMCase-V5-His was present in the periplasmic space with chitinolytic activity, which was measured using a chromogenic substrate, 4-nitrophenyl N,N′-diacetyl-β-D-chitobioside. The Protein A-AMCase-V5-His was purified from periplasmic fractions using an IgG Sepharose column followed by a Ni Sepharose chromatography. The recombinant protein showed a robust peak of activity with a maximum observed activity at pH 2.0, where an optimal temperature was 54°C. When this protein was preincubated between pH 1.0 and pH 11.0 on ice for 1 h, full chitinolytic activity was retained. This protein was also heat-stable till 54°C, both at pH 2.0 and 7.0. The chitinolytic activity of the recombinant AMCase against 4-nitrophenyl N,N′-diacetyl-β-D-chitobioside was comparable to the CHO-expressed AMCase. Furthermore, the recombinant AMCase bound to chitin beads, cleaved colloidal chitin and released mainly N,N′-diacetylchitobiose fragments. Thus, the E. coli-expressed Protein A-mouse AMCase-V5-His fusion protein possesses chitinase functions comparable to the CHO-expressed AMCase. This recombinant protein can be used to elucidate detailed biomedical functions of the mouse AMCase. PMID:24244337

  16. Comparative genomics for reliable protein-function prediction from genomic data.

    NARCIS (Netherlands)

    Huynen, M.A.; Snel, B.; Noort, V. van

    2004-01-01

    Genomic data provide invaluable, yet unreliable information about protein function. However, if the overlap in information among various genomic datasets is taken into account, one observes an increase in the reliability of the protein-function predictions that can be made. Recently published

  17. Systemic alterations in plasma proteins from women with chronic widespread pain compared to healthy controls: a proteomic study

    Directory of Open Access Journals (Sweden)

    Wåhlén K

    2017-04-01

    Full Text Available Karin Wåhlén, Patrik Olausson, Anders Carlsson, Nazdar Ghafouri, Björn Gerdle, Bijar Ghafouri Pain and Rehabilitation Centre, Department of Medical and Health Sciences, Linköping University, Linköping, Sweden Abstract: Chronic widespread pain (CWP is a complex pain condition that is difficult to treat. The prevalence of CWP approximates ~10% of the general population, with higher prevalence in women. Lack of understanding of molecular mechanisms has been a challenge for diagnosis and treatment of chronic pain. The aim of this study was to explore the systemic protein changes in CWP compared to those in healthy controls (CON. By applying 2-dimensional gel electrophoresis, we analyzed the protein pattern of plasma samples from women with CWP (n=16 and healthy women (n=23. The proteomic data were analyzed using multivariate statistical models, and altered proteins were identified using mass spectrometry. The proteome analysis was further validated by gel-free Western blot. Multivariate statistical data analysis of quantified proteins revealed 22 altered proteins in women with CWP, compared to CON group. Many of the identified proteins are previously known to be involved in different parts of the complement system and metabolic and inflammatory processes, e.g., complement factor B, vitamin D-binding protein, ceruloplasmin, transthyretin and alpha-2-HS-glycoprotein. These results indicate that important systemic protein differences exist between women with CWP and healthy women. Further, this study illustrates the potential use of proteomics to detect biomarkers that may provide new insights into the molecular mechanism(s of chronic pain. However, further larger investigations are required in order to confirm these findings before it will be possible to identify proteins as potential pain biomarkers for clinical use. Keywords: inflammation, biomarker, painomics, complement system, GC protein

  18. [Comparative Analysis of Spectrophotometric Methods of the Protein Measurement in the Pectic Polysaccharide Samples].

    Science.gov (United States)

    Ponomareva, S A; Golovchenko, V V; Patova, O A; Vanchikova, E V; Ovodov, Y S

    2015-01-01

    For the assay to reliability of determination of the protein content in the pectic polysaccharide samples by absorbance in the ultraviolet and visible regions of the spectrum a comparison of the eleven techniques called Flores, Lovry, Bradford, Sedmak, Rueman (ninhydrin reaction) methods, the method of ultraviolet spectrophotometry, the method Benedict's reagent, the method Nessler's reagent, the method with amide black, the bicinchoninic reagent and the biuret method was carried out. The data obtained show that insufficient sensitivity of the seven methods from the listed techniques doesn't allow their usage for determination of protein content in pectic polysaccharide samples. But the Lowry, Bradford, Sedmak methods, and the method Nessler's reagent may be used for determination of protein content in pectic polysaccharide samples, and the Bradford method is advisable for protein contaminants content determination in pectic polysaccharide samples in case protein content is less than 15%, and the Lowry method--for samples is more than 15%.

  19. Comparative assessment of fluorescent proteins for in vivo imaging in an animal model system.

    Science.gov (United States)

    Heppert, Jennifer K; Dickinson, Daniel J; Pani, Ariel M; Higgins, Christopher D; Steward, Annette; Ahringer, Julie; Kuhn, Jeffrey R; Goldstein, Bob

    2016-11-07

    Fluorescent protein tags are fundamental tools used to visualize gene products and analyze their dynamics in vivo. Recent advances in genome editing have expedited the precise insertion of fluorescent protein tags into the genomes of diverse organisms. These advances expand the potential of in vivo imaging experiments and facilitate experimentation with new, bright, photostable fluorescent proteins. Most quantitative comparisons of the brightness and photostability of different fluorescent proteins have been made in vitro, removed from biological variables that govern their performance in cells or organisms. To address the gap, we quantitatively assessed fluorescent protein properties in vivo in an animal model system. We generated transgenic Caenorhabditis elegans strains expressing green, yellow, or red fluorescent proteins in embryos and imaged embryos expressing different fluorescent proteins under the same conditions for direct comparison. We found that mNeonGreen was not as bright in vivo as predicted based on in vitro data but is a better tag than GFP for specific kinds of experiments, and we report on optimal red fluorescent proteins. These results identify ideal fluorescent proteins for imaging in vivo in C. elegans embryos and suggest good candidate fluorescent proteins to test in other animal model systems for in vivo imaging experiments. © 2016 Heppert et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  20. Comparative Analyses of Tomato yellow leaf curl virus C4 Protein-Interacting Host Proteins in Healthy and Infected Tomato Tissues

    Directory of Open Access Journals (Sweden)

    Namgyu Kim

    2016-10-01

    Full Text Available Tomato yellow leaf curl virus (TYLCV, a member of the genus Begomovirus, is one of the most important viruses of cultivated tomatoes worldwide, mainly causing yellowing and curling of leaves with stunting in plants. TYLCV causes severe problems in sub-tropical and tropical countries, as well as in Korea. However, the mechanism of TYLCV infection remains unclear, although the function of each viral component has been identified. TYLCV C4 codes for a small protein involved in various cellular functions, including symptom determination, gene silencing, viral movement, and induction of the plant defense response. In this study, through yeast-two hybrid screenings, we identified TYLCV C4-interacting host proteins from both healthy and symptom-exhibiting tomato tissues, to determine the role of TYLCV C4 proteins in the infection processes. Comparative analyses of 28 proteins from healthy tissues and 36 from infected tissues showing interactions with TYLCV C4 indicated that TYLCV C4 mainly interacts with host proteins involved in translation, ubiquitination, and plant defense, and most interacting proteins differed between the two tissues but belong to similar molecular functional categories. Four proteins—two ribosomal proteins, S-adenosyl-L-homocysteine hydrolase, and 14-3-3 family protein—were detected in both tissues. Furthermore, the identified proteins in symptom-exhibiting tissues showed greater involvement in plant defenses. Some are key regulators, such as receptor-like kinases and pathogenesis-related proteins, of plant defenses. Thus, TYLCV C4 may contribute to the suppression of host defense during TYLCV infection and be involved in ubiquitination for viral infection.

  1. transparent, a gene affecting stripe formation in Zebrafish, encodes the mitochondrial protein Mpv17 that is required for iridophore survival

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    Jana Krauss

    2013-06-01

    In the skin of adult zebrafish, three pigment cell types arrange into alternating horizontal stripes, melanophores in dark stripes, xanthophores in light interstripes and iridophores in both stripes and interstripes. The analysis of mutants and regeneration studies revealed that this pattern depends on interactions between melanophores and xanthophores; however, the role of iridophores in this process is less understood. We describe the adult viable and fertile mutant transparent (tra, which shows a loss or strong reduction of iridophores throughout larval and adult stages. In addition, in adults only the number of melanophores is strongly reduced, and stripes break up into spots. Stripes in the fins are normal. By cell transplantations we show that tra acts cell-autonomously in iridophores, whereas the reduction in melanophores in the body occurs secondarily as a consequence of iridophore loss. We conclude that differentiated iridophores are required for the accumulation and maintenance of melanophores during pigment pattern formation. The tra mutant phenotype is caused by a small deletion in mpv17, an ubiquituously expressed gene whose protein product, like its mammalian and yeast homologs, localizes to mitochondria. Iridophore death might be the result of mitochondrial dysfunction, consistent with the mitochondrial DNA depletion syndrome observed in mammalian mpv17 mutants. The specificity of the tra phenotype is most likely due to redundancy after gene multiplication, making this mutant a valuable model to understand the molecular function of Mpv17 in mitochondria.

  2. Comparative genomic analysis identified a mutation related to enhanced heterologous protein production in the filamentous fungus Aspergillus oryzae.

    Science.gov (United States)

    Jin, Feng-Jie; Katayama, Takuya; Maruyama, Jun-Ichi; Kitamoto, Katsuhiko

    2016-11-01

    Genomic mapping of mutations using next-generation sequencing technologies has facilitated the identification of genes contributing to fundamental biological processes, including human diseases. However, few studies have used this approach to identify mutations contributing to heterologous protein production in industrial strains of filamentous fungi, such as Aspergillus oryzae. In a screening of A. oryzae strains that hyper-produce human lysozyme (HLY), we previously isolated an AUT1 mutant that showed higher production of various heterologous proteins; however, the underlying factors contributing to the increased heterologous protein production remained unclear. Here, using a comparative genomic approach performed with whole-genome sequences, we attempted to identify the genes responsible for the high-level production of heterologous proteins in the AUT1 mutant. The comparative sequence analysis led to the detection of a gene (AO090120000003), designated autA, which was predicted to encode an unknown cytoplasmic protein containing an alpha/beta-hydrolase fold domain. Mutation or deletion of autA was associated with higher production levels of HLY. Specifically, the HLY yields of the autA mutant and deletion strains were twofold higher than that of the control strain during the early stages of cultivation. Taken together, these results indicate that combining classical mutagenesis approaches with comparative genomic analysis facilitates the identification of novel genes involved in heterologous protein production in filamentous fungi.

  3. Post-Exercise Muscle Protein Synthesis in Rats after Ingestion of Acidified Bovine Milk Compared with Skim Milk

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    Kyosuke Nakayama

    2017-09-01

    Full Text Available Bovine milk proteins have a low absorption rate due to gastric acid-induced coagulation. Acidified milk remains liquid under acidic conditions; therefore, the absorption rate of its protein may differ from that of untreated milk. To investigate how this would affect muscle protein synthesis (MPS, we compared MPS after ingestion of acidified versus skim milk in rats. Male Sprague-Dawley rats swam for 2 h and were immediately administered acidified or skim milk, then euthanized at 30, 60, 90, and 120 min afterwards. Triceps muscle samples were excised for assessing fractional synthetic rate (FSR, plasma components, intramuscular free amino acids and mTOR signaling. The FSR in the acidified milk group was significantly higher than in the skim milk group throughout the post-ingestive period. Plasma essential amino acids, leucine, and insulin levels were significantly increased in the acidified milk group at 30 min after administration compared to the skim milk group. In addition, acidified milk ingestion was associated with greater phosphorylation of protein kinase B (Akt and ribosomal protein S6 kinase (S6K1, and sustained phosphorylation of 4E-binding protein 1 (4E-BP1. These results indicate that compared with untreated milk, acidified milk ingestion is associated with greater stimulation of post-exercise MPS.

  4. ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes.

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    Bhasi, Ashwini; Philip, Philge; Manikandan, Vinu; Senapathy, Periannan

    2009-01-01

    We have developed ExDom, a unique database for the comparative analysis of the exon-intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon-intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon-intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon-intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/.

  5. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein.

    Science.gov (United States)

    Kankainen, Matti; Paulin, Lars; Tynkkynen, Soile; von Ossowski, Ingemar; Reunanen, Justus; Partanen, Pasi; Satokari, Reetta; Vesterlund, Satu; Hendrickx, Antoni P A; Lebeer, Sarah; De Keersmaecker, Sigrid C J; Vanderleyden, Jos; Hämäläinen, Tuula; Laukkanen, Suvi; Salovuori, Noora; Ritari, Jarmo; Alatalo, Edward; Korpela, Riitta; Mattila-Sandholm, Tiina; Lassig, Anna; Hatakka, Katja; Kinnunen, Katri T; Karjalainen, Heli; Saxelin, Maija; Laakso, Kati; Surakka, Anu; Palva, Airi; Salusjärvi, Tuomas; Auvinen, Petri; de Vos, Willem M

    2009-10-06

    To unravel the biological function of the widely used probiotic bacterium Lactobacillus rhamnosus GG, we compared its 3.0-Mbp genome sequence with the similarly sized genome of L. rhamnosus LC705, an adjunct starter culture exhibiting reduced binding to mucus. Both genomes demonstrated high sequence identity and synteny. However, for both strains, genomic islands, 5 in GG and 4 in LC705, punctuated the colinearity. A significant number of strain-specific genes were predicted in these islands (80 in GG and 72 in LC705). The GG-specific islands included genes coding for bacteriophage components, sugar metabolism and transport, and exopolysaccharide biosynthesis. One island only found in L. rhamnosus GG contained genes for 3 secreted LPXTG-like pilins (spaCBA) and a pilin-dedicated sortase. Using anti-SpaC antibodies, the physical presence of cell wall-bound pili was confirmed by immunoblotting. Immunogold electron microscopy showed that the SpaC pilin is located at the pilus tip but also sporadically throughout the structure. Moreover, the adherence of strain GG to human intestinal mucus was blocked by SpaC antiserum and abolished in a mutant carrying an inactivated spaC gene. Similarly, binding to mucus was demonstrated for the purified SpaC protein. We conclude that the presence of SpaC is essential for the mucus interaction of L. rhamnosus GG and likely explains its ability to persist in the human intestinal tract longer than LC705 during an intervention trial. The presence of mucus-binding pili on the surface of a nonpathogenic Gram-positive bacterial strain reveals a previously undescribed mechanism for the interaction of selected probiotic lactobacilli with host tissues.

  6. A vaccine formulation combining rhoptry proteins NcROP40 and NcROP2 improves pup survival in a pregnant mouse model of neosporosis.

    Science.gov (United States)

    Pastor-Fernández, Iván; Arranz-Solís, David; Regidor-Cerrillo, Javier; Álvarez-García, Gema; Hemphill, Andrew; García-Culebras, Alicia; Cuevas-Martín, Carmen; Ortega-Mora, Luis M

    2015-01-30

    Currently there are no effective vaccines for the control of bovine neosporosis. During the last years several subunit vaccines based on immunodominant antigens and other proteins involved in adhesion, invasion and intracellular proliferation of Neospora caninum have been evaluated as targets for vaccine development in experimental mouse infection models. Among them, the rhoptry antigen NcROP2 and the immunodominant NcGRA7 protein have been assessed with varying results. Recent studies have shown that another rhoptry component, NcROP40, and NcNTPase, a putative dense granule antigen, exhibit higher expression levels in tachyzoites of virulent N. caninum isolates, suggesting that these could be potential vaccine candidates to limit the effects of infection. In the present work, the safety and efficacy of these recombinant antigens formulated in Quil-A adjuvant as monovalent vaccines or pair-wise combinations (rNcROP40+rNcROP2 and rNcGRA7+rNcNTPase) were evaluated in a pregnant mouse model of neosporosis. All the vaccine formulations elicited a specific immune response against their respective native proteins after immunization. Mice vaccinated with rNcROP40 and rNcROP2 alone or in combination produced the highest levels of IFN-γ and exhibited low parasite burdens and low IgG antibody levels after the challenge. In addition, most of the vaccine formulations were able to increase the median survival time in the offspring. However, pup survival only ensued in the groups vaccinated with rNcROP40+rNcROP2 (16.2%) and rNcROP2 (6.3%). Interestingly, vertical transmission was not observed in those survivor pups immunized with rNcROP40+rNcROP2, as shown by PCR analyses. These results show a partial protection against N. caninum infection after vaccination with rNcROP40+rNcROP2, suggesting a synergistic effect of the two recombinant rhoptry antigens. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Increased Circulating Level of the Survival Factor GP88 (Progranulin in the Serum of Breast Cancer Patients When Compared to Healthy Subjects

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    Katherine Rak Tkaczuk

    2011-01-01

    Full Text Available Introduction GP88 (PC-Cell Derived Growth Factor, progranulin is a glycoprotein overexpressed in breast tumors and involved in their proliferation and survival. Since GP88 is secreted, an exploratory study was established to compare serum GP88 level between breast cancer patients (BC and healthy volunteers (HV. Methods An IRB approved prospective study enrolled 189 stage 1–4 BC patients and 18 HV. GP88 serum concentration was determined by immunoassay. Results Serum GP88 level was 28.7+ 5.8 ng/ml in HV and increased to 40.7+ 16.0 ng/ml ( P = 0.007 for stage 1-3 and 45.3 +23.3 ng/ml ( P = 0.0007 for stage 4 BC patients. There was no correlation between the GP88 level and BC characteristics such as age, race, tumor grade, ER, PR and HER-2 expression. Conclusion These data suggest that serial testing of serum GP88 levels may have value as a circulating biomarker for detection, monitoring and follow up of BC.

  8. Comprehensive comparative analysis and identification of RNA-binding protein domains: multi-class classification and feature selection.

    Science.gov (United States)

    Jahandideh, Samad; Srinivasasainagendra, Vinodh; Zhi, Degui

    2012-11-07

    RNA-protein interaction plays an important role in various cellular processes, such as protein synthesis, gene regulation, post-transcriptional gene regulation, alternative splicing, and infections by RNA viruses. In this study, using Gene Ontology Annotated (GOA) and Structural Classification of Proteins (SCOP) databases an automatic procedure was designed to capture structurally solved RNA-binding protein domains in different subclasses. Subsequently, we applied tuned multi-class SVM (TMCSVM), Random Forest (RF), and multi-class ℓ1/ℓq-regularized logistic regression (MCRLR) for analysis and classifying RNA-binding protein domains based on a comprehensive set of sequence and structural features. In this study, we compared prediction accuracy of three different state-of-the-art predictor methods. From our results, TMCSVM outperforms the other methods and suggests the potential of TMCSVM as a useful tool for facilitating the multi-class prediction of RNA-binding protein domains. On the other hand, MCRLR by elucidating importance of features for their contribution in predictive accuracy of RNA-binding protein domains subclasses, helps us to provide some biological insights into the roles of sequences and structures in protein-RNA interactions.

  9. Comparative Outer Membrane Protein Analysis of High and Low-Invasive Strains of Cronobacter malonaticus

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    Maha A. Aldubyan

    2017-11-01

    Full Text Available Cronobacter are an important group of foodborne pathogens that has been linked to life-threatening infections in both infants and adults. The major infections associated with Cronobacter species are neonatal meningitis, necrotizing enterocolitis, and septicaemia. There are seven species in the Cronobacter genus, of which only three are of clinical importance; Cronobacter sakazakii, Cronobacter malonaticus, and Cronobacter turicensis. To date most studies have focussed on C. sakazakii as it is the major species associated with neonatal infections. However, recently C. malonaticus, in particular sequence type 7 (ST7, has been noted as being prevalent in adult infections and therefore warranting further investigation. In this study, eight strains of C. malonaticus ST7, that had been isolated from a wide range of sources and varied in their in vitro virulence, were chosen for proteomic analysis of their outer membrane proteins (OMPs. One-dimensional gel analysis revealed a ~29 kDa size band that was only present in the highly invasive strains. Subsequent mass spectrometric analysis identified several peptides that matched the flagellin protein. The presence of flagellin protein was confirmed in 2D gel spot. Mass spectrometry analysis of total OMPs revealed that the four highly invasive C. malonaticus strains expressed the main flagellum proteins that were absent from the four low invasive strains. These were the flagellar hook protein FlgE, flagellar hook-associated protein 1, flagellar hook-associated protein, flagellin, and flagellar hook-filament junction protein FlgL. This data indicates that C. malonaticus flagellar proteins may have an important role in the organism's invasion properties.

  10. Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications

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    Huang Yong

    2009-11-01

    Full Text Available Abstract Background Gene and genome duplication is the principle creative force in evolution. Recently, protein subcellular relocalization, or neolocalization was proposed as one of the mechanisms responsible for the retention of duplicated genes. This hypothesis received support from the analysis of yeast genomes, but has not been tested thoroughly on animal genomes. In order to evaluate the importance of subcellular relocalizations for retention of duplicated genes in animal genomes, we systematically analyzed nuclear encoded mitochondrial proteins in the human genome by reconstructing phylogenies of mitochondrial multigene families. Results The 456 human mitochondrial proteins selected for this study were clustered into 305 gene families including 92 multigene families. Among the multigene families, 59 (64% consisted of both mitochondrial and cytosolic (non-mitochondrial proteins (mt-cy families while the remaining 33 (36% were composed of mitochondrial proteins (mt-mt families. Phylogenetic analyses of mt-cy families revealed three different scenarios of their neolocalization following gene duplication: 1 relocalization from mitochondria to cytosol, 2 from cytosol to mitochondria and 3 multiple subcellular relocalizations. The neolocalizations were most commonly enabled by the gain or loss of N-terminal mitochondrial targeting signals. The majority of detected subcellular relocalization events occurred early in animal evolution, preceding the evolution of tetrapods. Mt-mt protein families showed a somewhat different pattern, where gene duplication occurred more evenly in time. However, for both types of protein families, most duplication events appear to roughly coincide with two rounds of genome duplications early in vertebrate evolution. Finally, we evaluated the effects of inaccurate and incomplete annotation of mitochondrial proteins and found that our conclusion of the importance of subcellular relocalization after gene duplication on

  11. An implantable vascularized protein gel construct that supports human fetal hepatoblast survival and infection by hepatitis C virus in mice.

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    Martha J Harding

    2010-04-01

    Full Text Available Widely accessible small animal models suitable for the study of hepatitis C virus (HCV in vivo are lacking, primarily because rodent hepatocytes cannot be productively infected and because human hepatocytes are not easily engrafted in immunodeficient mice.We report here on a novel approach for human hepatocyte engraftment that involves subcutaneous implantation of primary human fetal hepatoblasts (HFH within a vascularized rat collagen type I/human fibronectin (rCI/hFN gel containing Bcl-2-transduced human umbilical vein endothelial cells (Bcl-2-HUVEC in severe combined immunodeficient X beige (SCID/bg mice. Maturing hepatic epithelial cells in HFH/Bcl-2-HUVEC co-implants displayed endocytotic activity at the basolateral surface, canalicular microvilli and apical tight junctions between adjacent cells assessed by transmission electron microscopy. Some primary HFH, but not Huh-7.5 hepatoma cells, appeared to differentiate towards a cholangiocyte lineage within the gels, based on histological appearance and cytokeratin 7 (CK7 mRNA and protein expression. Levels of human albumin and hepatic nuclear factor 4alpha (HNF4alpha mRNA expression in gel implants and plasma human albumin levels in mice engrafted with HFH and Bcl-2-HUVEC were somewhat enhanced by including murine liver-like basement membrane (mLBM components and/or hepatocyte growth factor (HGF-HUVEC within the gel matrix. Following ex vivo viral adsorption, both HFH/Bcl-2-HUVEC and Huh-7.5/Bcl-2-HUVEC co-implants sustained HCV Jc1 infection for at least 2 weeks in vivo, based on qRT-PCR and immunoelectron microscopic (IEM analyses of gel tissue.The system described here thus provides the basis for a simple and robust small animal model of HFH engraftment that is applicable to the study of HCV infections in vivo.

  12. Non-SMC condensin I complex proteins control chromosome segregation and survival of proliferating cells in the zebrafish neural retina

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    Harris William A

    2009-07-01

    Full Text Available Abstract Background The condensation of chromosomes and correct sister chromatid segregation during cell division is an essential feature of all proliferative cells. Structural maintenance of chromosomes (SMC and non-SMC proteins form the condensin I complex and regulate chromosome condensation and segregation during mitosis. However, due to the lack of appropriate mutants, the function of the condensin I complex during vertebrate development has not been described. Results Here, we report the positional cloning and detailed characterization of retinal phenotypes of a zebrafish mutation at the cap-g locus. High resolution live imaging reveals that the progression of mitosis between prometa- to telophase is delayed and that sister chromatid segregation is impaired upon loss of CAP-G. CAP-G associates with chromosomes between prometa- and telophase of the cell cycle. Loss of the interaction partners CAP-H and CAP-D2 causes cytoplasmic mislocalization of CAP-G throughout mitosis. DNA content analysis reveals increased genomic imbalances upon loss of non-SMC condensin I subunits. Within the retina, loss of condensin I function causes increased rates of apoptosis among cells within the proliferative ciliary marginal zone (CMZ whereas postmitotic retinal cells are viable. Inhibition of p53-mediated apoptosis partially rescues cell numbers in cap-g mutant retinae and allows normal layering of retinal cell types without alleviating their aberrant nuclear sizes. Conclusion Our findings indicate that the condensin I complex is particularly important within rapidly amplifying progenitor cell populations to ensure faithful chromosome segregation. In contrast, differentiation of postmitotic retinal cells is not impaired upon polyploidization.

  13. An implantable vascularized protein gel construct that supports human fetal hepatoblast survival and infection by hepatitis C virus in mice.

    Science.gov (United States)

    Harding, Martha J; Lepus, Christin M; Gibson, Thomas F; Shepherd, Benjamin R; Gerber, Scott A; Graham, Morven; Paturzo, Frank X; Rahner, Christoph; Madri, Joseph A; Bothwell, Alfred L M; Lindenbach, Brett D; Pober, Jordan S

    2010-04-01

    Widely accessible small animal models suitable for the study of hepatitis C virus (HCV) in vivo are lacking, primarily because rodent hepatocytes cannot be productively infected and because human hepatocytes are not easily engrafted in immunodeficient mice. We report here on a novel approach for human hepatocyte engraftment that involves subcutaneous implantation of primary human fetal hepatoblasts (HFH) within a vascularized rat collagen type I/human fibronectin (rCI/hFN) gel containing Bcl-2-transduced human umbilical vein endothelial cells (Bcl-2-HUVEC) in severe combined immunodeficient X beige (SCID/bg) mice. Maturing hepatic epithelial cells in HFH/Bcl-2-HUVEC co-implants displayed endocytotic activity at the basolateral surface, canalicular microvilli and apical tight junctions between adjacent cells assessed by transmission electron microscopy. Some primary HFH, but not Huh-7.5 hepatoma cells, appeared to differentiate towards a cholangiocyte lineage within the gels, based on histological appearance and cytokeratin 7 (CK7) mRNA and protein expression. Levels of human albumin and hepatic nuclear factor 4alpha (HNF4alpha) mRNA expression in gel implants and plasma human albumin levels in mice engrafted with HFH and Bcl-2-HUVEC were somewhat enhanced by including murine liver-like basement membrane (mLBM) components and/or hepatocyte growth factor (HGF)-HUVEC within the gel matrix. Following ex vivo viral adsorption, both HFH/Bcl-2-HUVEC and Huh-7.5/Bcl-2-HUVEC co-implants sustained HCV Jc1 infection for at least 2 weeks in vivo, based on qRT-PCR and immunoelectron microscopic (IEM) analyses of gel tissue. The system described here thus provides the basis for a simple and robust small animal model of HFH engraftment that is applicable to the study of HCV infections in vivo.

  14. Comparative studies on the photosensitizing potency of 5-methoxypsoralen and 8-methoxypsoralen as measured by cytolysis in Paramecium caudatam and Tetrahymena pyriformis, and growth inhibition and survival in Candida albicans

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    Young, A.R. (Institute of Dermatology, London (UK)); Barth, J. (Karl-Marx-Universitaet, Leipzig (German Democratic Republic))

    1982-01-01

    The photosensitizing potencies of 5-methoxypsoralen and 8-methoxypsoralen were investigated using the following biological end-points for lethality: (i) cytolysis in the protozoans Paramecium caudatum and Tetrahymena pyriformis, (ii) inhibition of growth in the yeast Candida albicans and (iii) survival as measured by colony counts in Candida albicans. In all cases, 5-methoxypsoralen proved to be the more potent photosensitizing agent. The preliminary action spectra of the 2 compounds for growth inhibition in C. albicans were similar and showed maximal spectral efficiency in the 320-340 nm waveband. The molecular basis for the described end-points is unknown. Although it is well known that 5-methoxypsoralen and 8-methoxypsoralen readily photoreact with DNA, it is considered that photoreaction with protein should also be given serious consideration as the possible lethal event. The superior effect of 5-methoxypsoralen is in accordance with some of the physical and photochemical properties of this molecule, but this result is at variance with other studies in different test systems that have been used to compare the photobiological efficacy of these 2 compounds.

  15. Comparative sperm protein profiling in bulls differing in fertility and identification of phosphatidylethanolamine-binding protein 4, a potential fertility marker.

    Science.gov (United States)

    Somashekar, L; Selvaraju, S; Parthipan, S; Patil, S K; Binsila, B K; Venkataswamy, M M; Karthik Bhat, S; Ravindra, J P

    2017-09-01

    This study aimed to identify sperm proteomic signatures regulating sperm functions and fertility by: (i) comparing the sperm electrophoretic protein profiles and identifying the differentially abundant proteins among breeding bulls differing in fertility status and (ii) elucidating the possible role of one of the identified novel proteins, PEBP4 on sperm function and fertility. The grouping of bulls as fertile (n = 6) and low fertile (n = 6) was performed based on bull fertility index and infertile (n = 6) based on semen rejection rate (>33%). The sperm motility, fructolysis index, acrosomal reaction, intracellular calcium levels, and seminal plasma fructose and calcium levels were studied among fertility groups. The differentially expressed sperm proteins observed in single- and two-dimensional gel electrophoresis (2DE) were identified using Nano-LC-MS/MS. In the fertile bulls, the expression levels of calmodulin (CALM1), spermadhesinZ13 (SPADH2), and phosphatidylethanolamine-binding protein 4 (PEBP4) were significantly (p sperm fructose uptake was observed. Further, PEBP4 was localized in elongated spermatids, Leydig cells, excurrent duct system, and principal piece of spermatozoa. These findings suggest a crucial role for the PEBP4 protein in spermiogenesis, epididymal sperm maturation, and sperm motility. This first study in bovine indicates the positive association of PEBP4 in regulating sperm maturation, functions, and fertility and could be a potential marker for predicting semen quality and fertility. © 2017 American Society of Andrology and European Academy of Andrology.

  16. Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades

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    Frohme Marcus

    2009-10-01

    Full Text Available Abstract Background Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. Results To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb as well as rapid COG search for function assignments including species-specific repositories of all analysed data. Conclusion Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.

  17. Comparative Long-term Study of a Large Series of Patients with Invasive Ductal Carcinoma and Invasive Lobular Carcinoma. Loco-Regional Recurrence, Metastasis, and Survival.

    Science.gov (United States)

    García-Fernández, Antonio; Lain, Josep María; Chabrera, Carol; García Font, Marc; Fraile, Manel; Barco, Israel; Torras, Merçe; Reñe, Asumpta; González, Sonia; González, Clarissa; Piqueras, Mercedes; Veloso, Enrique; Cirera, Lluís; Pessarrodona, Antoni; Giménez, Nuria

    2015-01-01

    Our aim was to compare histologic and immunohistochemical features, surgical treatment and clinical course, including disease recurrence, distant metastases, and mortality between patients with invasive ductal carcinoma (IDC) or invasive lobular carcinoma (ILC). We included 1,745 patients operated for 1,789 breast tumors, with 1,639 IDC (1,600 patients) and 145 patients with ILC and 150 breast tumors. The median follow-up was 76 months. ILC was significantly more likely to be associated with a favorable phenotype. Prevalence of contralateral breast cancer was slightly higher for ILC patients than for IDC patients (4.0% versus 3.2%; p = n.s). ILC was more likely multifocal, estrogen receptor positive, Human Epidermal Growth Factor Receptor-2 (HER2) negative, and with lower proliferative index compared to IDC. Considering conservative surgery, ILC patients required more frequently re-excision and/or mastectomy. Prevalence of stage IIB and III stages were significantly more frequent in ILC patients than in IDC patients (37.4% versus 25.3%, p = 0.006). Positive nodes were significantly more frequent in the ILC patients (44.6% versus 37.0%, p = 0.04). After adjustment for tumor size and nodal status, frequencies of recurrence/metastasis, disease-free and specific survival were similar among patients with IDC and patients with ILC. In conclusion, women with ILC do not have worse clinical outcomes than their counterparts with IDC. Management decisions should be based on individual patient and tumor biologic characteristics rather than on lobular versus ductal histology. © 2015 Wiley Periodicals, Inc.

  18. Inhibition of protein synthesis on the ribosome by tildipirosin compared with other veterinary macrolides

    DEFF Research Database (Denmark)

    Andersen, Niels Møller; Poehlsgaard, Jacob; Warrass, Ralf

    2012-01-01

    Tildipirosin is a 16-membered-ring macrolide developed to treat bacterial pathogens, including Mannheimia haemolytica and Pasteurella multocida, that cause respiratory tract infections in cattle and swine. Here we evaluated the efficacy of tildipirosin at inhibiting protein synthesis...

  19. The water extract of Liuwei dihuang possesses multi-protective properties on neurons and muscle tissue against deficiency of survival motor neuron protein.

    Science.gov (United States)

    Tseng, Yu-Ting; Jong, Yuh-Jyh; Liang, Wei-Fang; Chang, Fang-Rong; Lo, Yi-Ching

    2017-10-15

    Deficiency of survival motor neuron (SMN) protein, which is encoded by the SMN1 and SMN2 genes, induces widespread splicing defects mainly in spinal motor neurons, and leads to spinal muscular atrophy (SMA). Currently, there is no effective treatment for SMA. Liuwei dihuang (LWDH), a traditional Chinese herbal formula, possesses multiple therapeutic benefits against various diseases via modulation of the nervous, immune and endocrine systems. Previously, we demonstrated water extract of LWDH (LWDH-WE) protects dopaminergic neurons and improves motor activity in models of Parkinson's disease. This study aimed to investigate the potential protection of LWDH-WE on SMN deficiency-induced neurodegeneration and muscle weakness. The effects of LWDH-WE on SMN deficiency-induced neurotoxicity and muscle atrophy were examined by using SMN-deficient NSC34 motor neuron-like cells and SMA-like mice, respectively. Inducible SMN-knockdown NSC34 motor neuron-like cells were used to mimic SMN-deficient condition. Doxycycline (1 µg/ml) was used to induce SMN deficiency in stable NSC34 cell line carrying SMN-specific shRNA. SMAΔ7 mice were used as a severe type of SMA mouse model. Cell viability was measured by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT) and lactate dehydrogenase (LDH) assays. Apoptotic cells and neurite length were observed by inverted microscope. Protein expressions were examined by western blots. Muscle strength of animals was evaluated by hind-limb suspension test. LWDH-WE significantly increased SMN protein level, mitochondrial membrane potential and cell viability of SMN-deficient NSC34 cells. LWDH-WE attenuated SMN deficiency-induced down-regulation of B-cell lymphoma-2 (Bcl-2) and up-regulation of cytosolic cytochrome c and cleaved caspase-3. Moreover, LWDH-WE prevented SMN deficiency-induced inhibition of neurite outgrowth and activation of Ras homolog gene family, member A (RhoA)/ Rho-associated protein kinase (ROCK2)/ phospho

  20. Comparative proteomic analysis of human whole saliva of children with protein-energy undernutrition.

    Science.gov (United States)

    Fonteles, Cristiane Sá Roriz; Dos Santos, Cláudia Ferreira; da Silva Alves, Karla Shangela; de Miranda Mota, Ana Catarina; Damasceno, Juliana Ximenes; Fonteles, Manassés Claudino

    2012-07-01

    The aim of the present study was to investigate the protein profile of children with different levels of protein-energy undernutrition (PEU) through a proteomic approach of human whole saliva. Initially, saliva sample